4UB8

Native structure of photosystem II (dataset-2) by a femtosecond X-ray laser


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Free: 0.225 
  • R-Value Work: 0.188 
  • R-Value Observed: 0.189 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 3.1 of the entry. See complete history


Literature

Native structure of photosystem II at 1.95 angstrom resolution viewed by femtosecond X-ray pulses.

Suga, M.Akita, F.Hirata, K.Ueno, G.Murakami, H.Nakajima, Y.Shimizu, T.Yamashita, K.Yamamoto, M.Ago, H.Shen, J.R.

(2015) Nature 517: 99-103

  • DOI: https://doi.org/10.1038/nature13991
  • Primary Citation of Related Structures:  
    4UB6, 4UB8

  • PubMed Abstract: 

    Photosynthesis converts light energy into biologically useful chemical energy vital to life on Earth. The initial reaction of photosynthesis takes place in photosystem II (PSII), a 700-kilodalton homodimeric membrane protein complex that catalyses photo-oxidation of water into dioxygen through an S-state cycle of the oxygen evolving complex (OEC). The structure of PSII has been solved by X-ray diffraction (XRD) at 1.9 ångström resolution, which revealed that the OEC is a Mn4CaO5-cluster coordinated by a well defined protein environment. However, extended X-ray absorption fine structure (EXAFS) studies showed that the manganese cations in the OEC are easily reduced by X-ray irradiation, and slight differences were found in the Mn-Mn distances determined by XRD, EXAFS and theoretical studies. Here we report a 'radiation-damage-free' structure of PSII from Thermosynechococcus vulcanus in the S1 state at a resolution of 1.95 ångströms using femtosecond X-ray pulses of the SPring-8 ångström compact free-electron laser (SACLA) and hundreds of large, highly isomorphous PSII crystals. Compared with the structure from XRD, the OEC in the X-ray free electron laser structure has Mn-Mn distances that are shorter by 0.1-0.2 ångströms. The valences of each manganese atom were tentatively assigned as Mn1D(III), Mn2C(IV), Mn3B(IV) and Mn4A(III), based on the average Mn-ligand distances and analysis of the Jahn-Teller axis on Mn(III). One of the oxo-bridged oxygens, O5, has significantly longer distances to Mn than do the other oxo-oxygen atoms, suggesting that O5 is a hydroxide ion instead of a normal oxygen dianion and therefore may serve as one of the substrate oxygen atoms. These findings provide a structural basis for the mechanism of oxygen evolution, and we expect that this structure will provide a blueprint for the design of artificial catalysts for water oxidation.


  • Organizational Affiliation

    Photosynthesis Research Center, Graduate School of Natural Science and Technology, Okayama University, 3-1-1 Tsushima Naka, Okayama 700-8530, Japan.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem Q(B) proteinA,
U [auth a]
344Thermostichus vulcanusMutation(s): 0 
EC: 1.10.3.9
Membrane Entity: Yes 
UniProt
Find proteins for P51765 (Thermostichus vulcanus)
Explore P51765 
Go to UniProtKB:  P51765
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP51765
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem II CP47 chlorophyll apoproteinB,
V [auth b]
505Thermostichus vulcanusMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for D0VWR1 (Thermostichus vulcanus)
Explore D0VWR1 
Go to UniProtKB:  D0VWR1
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupD0VWR1
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem II 44 kDa reaction center proteinC,
W [auth c]
455Thermostichus vulcanusMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for D0VWR7 (Thermostichus vulcanus)
Explore D0VWR7 
Go to UniProtKB:  D0VWR7
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupD0VWR7
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem II D2 proteinD,
X [auth d]
342Thermostichus vulcanusMutation(s): 0 
EC: 1.10.3.9
Membrane Entity: Yes 
UniProt
Find proteins for D0VWR8 (Thermostichus vulcanus)
Explore D0VWR8 
Go to UniProtKB:  D0VWR8
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupD0VWR8
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome b559 subunit alphaE,
Y [auth e]
84Thermostichus vulcanusMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for P12238 (Thermostichus vulcanus)
Explore P12238 
Go to UniProtKB:  P12238
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP12238
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome b559 subunit betaF,
Z [auth f]
44Thermostichus vulcanusMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for P12239 (Thermostichus vulcanus)
Explore P12239 
Go to UniProtKB:  P12239
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP12239
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem II reaction center protein HAA [auth h],
G [auth H]
65Thermostichus vulcanusMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for P19052 (Thermostichus vulcanus)
Explore P19052 
Go to UniProtKB:  P19052
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP19052
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem II reaction center protein IBA [auth i],
H [auth I]
38Thermostichus vulcanusMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for P12240 (Thermostichus vulcanus)
Explore P12240 
Go to UniProtKB:  P12240
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP12240
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem II reaction center protein JCA [auth j],
I [auth J]
39Thermostichus vulcanusMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for Q7DGD4 (Thermostichus vulcanus)
Explore Q7DGD4 
Go to UniProtKB:  Q7DGD4
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ7DGD4
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem II reaction center protein KDA [auth k],
J [auth K]
37Thermostichus vulcanusMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for P19054 (Thermostichus vulcanus)
Explore P19054 
Go to UniProtKB:  P19054
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP19054
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem II reaction center protein LEA [auth l],
K [auth L]
37Thermostichus vulcanusMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for P12241 (Thermostichus vulcanus)
Explore P12241 
Go to UniProtKB:  P12241
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP12241
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem II reaction center protein MFA [auth m],
L [auth M]
36Thermostichus vulcanusMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for P12312 (Thermostichus vulcanus)
Explore P12312 
Go to UniProtKB:  P12312
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP12312
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem II manganese-stabilizing polypeptideGA [auth o],
M [auth O]
244Thermostichus vulcanusMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for D0VWR2 (Thermostichus vulcanus)
Explore D0VWR2 
Go to UniProtKB:  D0VWR2
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupD0VWR2
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem II reaction center protein THA [auth t],
N [auth T]
31Thermostichus vulcanusMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for P12313 (Thermostichus vulcanus)
Explore P12313 
Go to UniProtKB:  P12313
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP12313
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 15
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem II 12 kDa extrinsic proteinIA [auth u],
O [auth U]
104Thermostichus vulcanusMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for P56152 (Thermostichus vulcanus)
Explore P56152 
Go to UniProtKB:  P56152
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP56152
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 16
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome c-550JA [auth v],
P [auth V]
137Thermostichus vulcanusMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for P0A387 (Thermostichus vulcanus)
Explore P0A387 
Go to UniProtKB:  P0A387
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0A387
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 17
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem II reaction center protein Ycf12KA [auth y],
Q [auth Y]
30Thermostichus vulcanusMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for D0VWR3 (Thermostichus vulcanus)
Explore D0VWR3 
Go to UniProtKB:  D0VWR3
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupD0VWR3
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 18
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem II reaction center protein XLA [auth x],
R [auth X]
40Thermostichus vulcanusMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for D0VWR4 (Thermostichus vulcanus)
Explore D0VWR4 
Go to UniProtKB:  D0VWR4
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupD0VWR4
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 19
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem II reaction center protein ZMA [auth z],
S [auth Z]
62Thermostichus vulcanusMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for D0VWR5 (Thermostichus vulcanus)
Explore D0VWR5 
Go to UniProtKB:  D0VWR5
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupD0VWR5
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 20
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem II protein YT [auth R]34Thermostichus vulcanusMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for P0DM37 (Thermostichus vulcanus)
Explore P0DM37 
Go to UniProtKB:  P0DM37
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0DM37
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 20 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
DGD
Query on DGD

Download Ideal Coordinates CCD File 
BI [auth c]
CI [auth c]
DI [auth c]
FD [auth C]
GD [auth C]
BI [auth c],
CI [auth c],
DI [auth c],
FD [auth C],
GD [auth C],
GJ [auth h],
HD [auth C],
JE [auth H],
SI [auth d],
VD [auth D]
DIGALACTOSYL DIACYL GLYCEROL (DGDG)
C51 H96 O15
LDQFLSUQYHBXSX-HXXRYREZSA-N
CLA
Query on CLA

Download Ideal Coordinates CCD File 
AD [auth C]
BD [auth C]
CD [auth C]
HB [auth B]
IB [auth B]
AD [auth C],
BD [auth C],
CD [auth C],
HB [auth B],
IB [auth B],
IG [auth b],
JB [auth B],
JG [auth b],
KB [auth B],
KG [auth b],
LB [auth B],
LG [auth b],
MB [auth B],
MG [auth b],
MI [auth d],
NB [auth B],
NG [auth b],
NH [auth c],
NI [auth d],
OB [auth B],
OG [auth b],
OH [auth c],
PB [auth B],
PD [auth D],
PG [auth b],
PH [auth c],
PI [auth d],
QB [auth B],
QC [auth C],
QF [auth a],
QG [auth b],
QH [auth c],
RA [auth A],
RB [auth B],
RC [auth C],
RD [auth D],
RF [auth a],
RG [auth b],
RH [auth c],
SA [auth A],
SB [auth B],
SC [auth C],
SD [auth D],
SG [auth b],
SH [auth c],
TB [auth B],
TC [auth C],
TF [auth a],
TG [auth b],
TH [auth c],
UB [auth B],
UC [auth C],
UG [auth b],
UH [auth c],
VA [auth A],
VB [auth B],
VC [auth C],
VG [auth b],
VH [auth c],
WB [auth B],
WC [auth C],
WG [auth b],
WH [auth c],
XC [auth C],
XG [auth b],
XH [auth c],
YC [auth C],
YH [auth c],
ZC [auth C],
ZH [auth c]
CHLOROPHYLL A
C55 H72 Mg N4 O5
ATNHDLDRLWWWCB-AENOIHSZSA-M
PHO
Query on PHO

Download Ideal Coordinates CCD File 
OI [auth d],
SF [auth a],
TA [auth A],
UA [auth A]
PHEOPHYTIN A
C55 H74 N4 O5
CQIKWXUXPNUNDV-RCBXBCQGSA-N
SQD
Query on SQD

Download Ideal Coordinates CCD File 
BJ [auth f]
CB [auth A]
DG [auth b]
FE [auth F]
MF [auth a]
BJ [auth f],
CB [auth A],
DG [auth b],
FE [auth F],
MF [auth a],
OJ [auth l],
VF [auth a],
XA [auth A]
1,2-DI-O-ACYL-3-O-[6-DEOXY-6-SULFO-ALPHA-D-GLUCOPYRANOSYL]-SN-GLYCEROL
C41 H78 O12 S
RVUUQPKXGDTQPG-JUDHQOGESA-N
LMG
Query on LMG

Download Ideal Coordinates CCD File 
AC [auth B]
BH [auth b]
EI [auth c]
EK [auth z]
FI [auth c]
AC [auth B],
BH [auth b],
EI [auth c],
EK [auth z],
FI [auth c],
ID [auth C],
IJ [auth j],
JD [auth C],
KF [auth Z],
LH [auth c],
ME [auth J],
PC [auth C]
1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE
C45 H86 O10
DCLTVZLYPPIIID-CVELTQQQSA-N
PL9
Query on PL9

Download Ideal Coordinates CCD File 
AG [auth a],
FB [auth A],
RI [auth d],
UD [auth D]
2,3-DIMETHYL-5-(3,7,11,15,19,23,27,31,35-NONAMETHYL-2,6,10,14,18,22,26,30,34-HEXATRIACONTANONAENYL-2,5-CYCLOHEXADIENE-1,4-DIONE-2,3-DIMETHYL-5-SOLANESYL-1,4-BENZOQUINONE
C53 H80 O2
FKUYMLZIRPABFK-UHFFFAOYSA-N
LHG
Query on LHG

Download Ideal Coordinates CCD File 
CE [auth E]
PJ [auth l]
QE [auth L]
TI [auth d]
UI [auth d]
CE [auth E],
PJ [auth l],
QE [auth L],
TI [auth d],
UI [auth d],
VI [auth d],
WD [auth D],
XD [auth D],
YD [auth D],
ZI [auth e]
1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE
C38 H75 O10 P
BIABMEZBCHDPBV-MPQUPPDSSA-N
HEC
Query on HEC

Download Ideal Coordinates CCD File 
CF [auth V],
YJ [auth v]
HEME C
C34 H34 Fe N4 O4
HXQIYSLZKNYNMH-LJNAALQVSA-N
HEM
Query on HEM

Download Ideal Coordinates CCD File 
AJ [auth e],
EE [auth E]
PROTOPORPHYRIN IX CONTAINING FE
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
BCR
Query on BCR

Download Ideal Coordinates CCD File 
AH [auth b]
AI [auth c]
CK [auth y]
DD [auth C]
ED [auth C]
AH [auth b],
AI [auth c],
CK [auth y],
DD [auth C],
ED [auth C],
FJ [auth h],
IE [auth H],
IF [auth Y],
KI [auth c],
NJ [auth k],
PE [auth K],
QI [auth d],
TD [auth D],
UF [auth a],
UJ [auth t],
WA [auth A],
XB [auth B],
YB [auth B],
YE [auth T],
YG [auth b],
ZB [auth B],
ZG [auth b]
BETA-CAROTENE
C40 H56
OENHQHLEOONYIE-JLTXGRSLSA-N
LMT
Query on LMT

Download Ideal Coordinates CCD File 
BG [auth a]
CH [auth b]
CJ [auth f]
DB [auth A]
DE [auth E]
BG [auth a],
CH [auth b],
CJ [auth f],
DB [auth A],
DE [auth E],
EG [auth b],
LE [auth I],
LF [auth a],
NC [auth B],
QD [auth D],
RE [auth M],
RJ [auth m],
SE [auth M],
SJ [auth m]
DODECYL-BETA-D-MALTOSIDE
C24 H46 O11
NLEBIOOXCVAHBD-QKMCSOCLSA-N
OEX
Query on OEX

Download Ideal Coordinates CCD File 
EB [auth A],
ZF [auth a]
CA-MN4-O5 CLUSTER
Ca Mn4 O5
SEXWDHMBWJEXOJ-UHFFFAOYSA-N
HTG
Query on HTG

Download Ideal Coordinates CCD File 
BC [auth B]
CC [auth B]
DC [auth B]
DF [auth V]
DH [auth b]
BC [auth B],
CC [auth B],
DC [auth B],
DF [auth V],
DH [auth b],
EH [auth b],
FG [auth b],
GG [auth b],
GI [auth c],
HI [auth c],
JC [auth B],
KC [auth B],
KD [auth C],
LD [auth C],
WE [auth O],
WI [auth d],
ZD [auth D]
heptyl 1-thio-beta-D-glucopyranoside
C13 H26 O5 S
HPEGNLMTTNTJSP-LBELIVKGSA-N
GOL
Query on GOL

Download Ideal Coordinates CCD File 
AB [auth A]
AF [auth V]
AK [auth v]
BK [auth v]
EC [auth B]
AB [auth A],
AF [auth V],
AK [auth v],
BK [auth v],
EC [auth B],
EF [auth V],
EJ [auth f],
FC [auth B],
FF [auth V],
FH [auth b],
GC [auth B],
GF [auth V],
GH [auth b],
HC [auth B],
HE [auth F],
HF [auth V],
HH [auth b],
IC [auth B],
IH [auth b],
II [auth c],
JH [auth b],
JI [auth c],
LI [auth c],
MC [auth B],
MD [auth C],
ND [auth C],
OC [auth B],
VE [auth O],
VJ [auth t],
WF [auth a],
XE [auth T],
XF [auth a],
XJ [auth v],
YA [auth A],
ZA [auth A],
ZE [auth T],
ZJ [auth v]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
BCT
Query on BCT

Download Ideal Coordinates CCD File 
CG [auth a],
QA [auth A]
BICARBONATE ION
C H O3
BVKZGUZCCUSVTD-UHFFFAOYSA-M
FE2
Query on FE2

Download Ideal Coordinates CCD File 
NA [auth A],
NF [auth a]
FE (II) ION
Fe
CWYNVVGOOAEACU-UHFFFAOYSA-N
CA
Query on CA

Download Ideal Coordinates CCD File 
DJ [auth f]
GB [auth B]
GE [auth F]
HG [auth b]
MH [auth c]
DJ [auth f],
GB [auth B],
GE [auth F],
HG [auth b],
MH [auth c],
TJ [auth o],
UE [auth O]
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
CL
Query on CL

Download Ideal Coordinates CCD File 
BF [auth V]
OA [auth A]
OF [auth a]
PA [auth A]
PF [auth a]
BF [auth V],
OA [auth A],
OF [auth a],
PA [auth A],
PF [auth a],
WJ [auth u]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
MG
Query on MG

Download Ideal Coordinates CCD File 
JJ [auth j],
NE [auth J]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
UNL
Query on UNL

Download Ideal Coordinates CCD File 
AE [auth D]
BB [auth A]
BE [auth D]
DK [auth x]
HJ [auth i]
AE [auth D],
BB [auth A],
BE [auth D],
DK [auth x],
HJ [auth i],
JF [auth X],
KE [auth I],
KH [auth b],
KJ [auth j],
LC [auth B],
LJ [auth k],
MJ [auth k],
OD [auth C],
OE [auth J],
QJ [auth m],
TE [auth M],
XI [auth d],
YF [auth a],
YI [auth d]
Unknown ligand
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
FME
Query on FME
BA [auth i],
H [auth I]
L-PEPTIDE LINKINGC6 H11 N O3 SMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Free: 0.225 
  • R-Value Work: 0.188 
  • R-Value Observed: 0.189 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 123.807α = 90
b = 230.001β = 90
c = 288.502γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2014-12-03
    Type: Initial release
  • Version 1.1: 2015-04-15
    Changes: Database references
  • Version 1.2: 2017-07-26
    Changes: Advisory, Data collection, Database references, Derived calculations, Source and taxonomy
  • Version 2.0: 2019-10-02
    Changes: Atomic model, Data collection, Derived calculations, Non-polymer description, Structure summary
  • Version 2.1: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Derived calculations, Structure summary
  • Version 3.0: 2024-03-20
    Changes: Data collection, Database references, Non-polymer description, Source and taxonomy, Structure summary
  • Version 3.1: 2024-10-23
    Changes: Structure summary