5ZF0

X-ray Structure of the Electron Transfer Complex between Ferredoxin and Photosystem I

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 4.20 Å
  • R-Value Free: 0.377 
  • R-Value Work: 0.353 
  • R-Value Observed: 0.354 

Starting Model: experimental
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This is version 2.1 of the entry. See complete history. 


Literature

X-ray structure of an asymmetrical trimeric ferredoxin-photosystem I complex

Kubota-Kawai, H., Mutoh, R., Shinmura, K., Setif, P., Nowaczyk, M.M., Rogner, M., Ikegami, T., Tanaka, H., Kurisu, G.

(2018) Nat Plants 4: 218-224

  • DOI: https://doi.org/10.1038/s41477-018-0130-0
  • Primary Citation of Related Structures:  
    5ZF0

  • PubMed Abstract: 

    Photosystem I (PSI), a large protein complex located in the thylakoid membrane, mediates the final step in light-driven electron transfer to the stromal electron carrier protein ferredoxin (Fd). Here, we report the first structural description of the PSI-Fd complex from Thermosynechococcus elongatus. The trimeric PSI complex binds three Fds in a non-equivalent manner. While each is recognized by a PSI protomer in a similar orientation, the distances between Fds and the PSI redox centres differ. Fd binding thus entails loss of the exact three-fold symmetry of the PSI's soluble subunits, inducing structural perturbations which are transferred to the lumen through PsaF. Affinity chromatography and nuclear magnetic resonance analyses of PSI-Fd complexes support the existence of two different Fd-binding states, with one Fd being more tightly bound than the others. We propose a dynamic structural basis for productive complex formation, which supports fast electron transfer between PSI and Fd.

    • Organizational Affiliation: 

    Institute for Protein Research, Osaka University, Osaka, Japan.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem I P700 chlorophyll a apoprotein A1755Thermosynechococcus vestitus BP-1Mutation(s): 0 
EC: 1.97.1.12
Membrane Entity: Yes 
UniProt
Find proteins for P0A405 (Thermosynechococcus vestitus (strain NIES-2133 / IAM M-273 / BP-1))
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem I P700 chlorophyll a apoprotein A2740Thermosynechococcus vestitus BP-1Mutation(s): 0 
EC: 1.97.1.12
Membrane Entity: Yes 
UniProt
Find proteins for P0A407 (Thermosynechococcus vestitus (strain NIES-2133 / IAM M-273 / BP-1))
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem I iron-sulfur center80Thermosynechococcus vestitus BP-1Mutation(s): 0 
EC: 1.97.1.12
Membrane Entity: Yes 
UniProt
Find proteins for P0A415 (Thermosynechococcus vestitus (strain NIES-2133 / IAM M-273 / BP-1))
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem I reaction center subunit II138Thermosynechococcus vestitus BP-1Mutation(s): 0 
UniProt
Find proteins for P0A420 (Thermosynechococcus vestitus (strain NIES-2133 / IAM M-273 / BP-1))
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem I reaction center subunit IV75Thermosynechococcus vestitus BP-1Mutation(s): 0 
Membrane Entity: Yes 
UniProt
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem I reaction center subunit III164Thermosynechococcus vestitus BP-1Mutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for P0A401 (Thermosynechococcus vestitus (strain NIES-2133 / IAM M-273 / BP-1))
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem I reaction center subunit VIII38Thermosynechococcus vestitus BP-1Mutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for P0A427 (Thermosynechococcus vestitus (strain NIES-2133 / IAM M-273 / BP-1))
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem I reaction center subunit IX41Thermosynechococcus vestitus BP-1Mutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for P0A429 (Thermosynechococcus vestitus (strain NIES-2133 / IAM M-273 / BP-1))
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem I reaction center subunit PsaK83Thermosynechococcus vestitus BP-1Mutation(s): 0 
Membrane Entity: Yes 
UniProt
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem I reaction center subunit XI154Thermosynechococcus vestitus BP-1Mutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for Q8DGB4 (Thermosynechococcus vestitus (strain NIES-2133 / IAM M-273 / BP-1))
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem I reaction center subunit XII31Thermosynechococcus vestitus BP-1Mutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for P0A403 (Thermosynechococcus vestitus (strain NIES-2133 / IAM M-273 / BP-1))
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
PsaX35Thermosynechococcus vestitusMutation(s): 0 
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
Ferredoxin-197Thermosynechococcus vestitus BP-1Mutation(s): 0 
Gene Names: petF1, petF, tsl1009
UniProt
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Small Molecules
Ligands 8 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
CLA
Query on CLA
Download Ideal Coordinates CCD File 
AAA [auth J6]
ABA [auth A5]
AC [auth A1]
ACA [auth A5]
AD [auth A1]
AAA [auth J6],
ABA [auth A5],
AC [auth A1],
ACA [auth A5],
AD [auth A1],
ADA [auth B5],
AE [auth B1],
AEA [auth B5],
AF [auth B1],
AH [auth A2],
AI [auth A2],
AK [auth B2],
AM [auth A3],
AN [auth A3],
AO [auth B3],
AP [auth B3],
AR [auth A4],
AS [auth A4],
AT [auth B4],
AU [auth B4],
AW [auth A6],
AX [auth A6],
AY [auth B6],
AZ [auth B6],
BBA [auth A5],
BC [auth A1],
BCA [auth A5],
BD [auth A1],
BDA [auth B5],
BE [auth B1],
BEA [auth B5],
BF [auth B1],
BH [auth A2],
BI [auth A2],
BJ [auth B2],
BK [auth B2],
BM [auth A3],
BN [auth A3],
BO [auth B3],
BP [auth B3],
BQ [auth F3],
BR [auth A4],
BS [auth A4],
BT [auth B4],
BU [auth B4],
BW [auth A6],
BX [auth A6],
BY [auth B6],
BZ [auth B6],
CBA [auth A5],
CC [auth A1],
CCA [auth A5],
CD [auth A1],
CDA [auth B5],
CE [auth B1],
CEA [auth B5],
CF [auth B1],
CFA [auth K5],
CG [auth F1],
CH [auth A2],
CI [auth A2],
CJ [auth B2],
CK [auth B2],
CL [auth F2],
CM [auth A3],
CN [auth A3],
CO [auth B3],
CP [auth B3],
CR [auth A4],
CS [auth A4],
CT [auth B4],
CU [auth B4],
CW [auth A6],
CX [auth A6],
CY [auth B6],
CZ [auth B6],
DAA [auth K6],
DBA [auth A5],
DC [auth A1],
DCA [auth A5],
DD [auth A1],
DDA [auth B5],
DE [auth B1],
DEA [auth B5],
DF [auth B1],
DFA [auth K5],
DH [auth A2],
DI [auth A2],
DJ [auth B2],
DK [auth B2],
DM [auth A3],
DN [auth A3],
DO [auth B3],
DP [auth B3],
DR [auth A4],
DS [auth A4],
DT [auth B4],
DU [auth B4],
DV [auth J4],
DW [auth A6],
DX [auth A6],
DY [auth B6],
DZ [auth B6],
EBA [auth A5],
EC [auth A1],
ECA [auth A5],
ED [auth A1],
EDA [auth B5],
EE [auth B1],
EEA [auth B5],
EF [auth B1],
EG [auth I1],
EH [auth A2],
EI [auth A2],
EJ [auth B2],
EK [auth B2],
EL [auth F2],
EM [auth A3],
EN [auth A3],
EO [auth B3],
EP [auth B3],
ER [auth A4],
ES [auth A4],
ET [auth B4],
EU [auth B4],
EV [auth J4],
EW [auth A6],
EX [auth A6],
EY [auth B6],
EZ [auth B6],
FAA [auth L6],
FBA [auth A5],
FC [auth A1],
FCA [auth A5],
FD [auth A1],
FDA [auth B5],
FE [auth B1],
FEA [auth B5],
FF [auth B1],
FFA [auth L5],
FH [auth A2],
FI [auth A2],
FJ [auth B2],
FK [auth B2],
FM [auth A3],
FN [auth A3],
FO [auth B3],
FP [auth B3],
FQ [auth J3],
FR [auth A4],
FS [auth A4],
FT [auth B4],
FU [auth B4],
FW [auth A6],
FX [auth A6],
FY [auth B6],
FZ [auth B6],
GAA [auth L6],
GBA [auth A5],
GC [auth A1],
GCA [auth A5],
GD [auth A1],
GDA [auth B5],
GE [auth B1],
GEA [auth B5],
GF [auth B1],
GFA [auth L5],
GH [auth A2],
GI [auth A2],
GJ [auth B2],
GK [auth B2],
GL [auth J2],
GM [auth A3],
GN [auth A3],
GO [auth B3],
GP [auth B3],
GQ [auth J3],
GR [auth A4],
GS [auth A4],
GT [auth B4],
GU [auth B4],
GW [auth A6],
GX [auth A6],
GY [auth B6],
GZ [auth B6],
HBA [auth A5],
HC [auth A1],
HD [auth A1],
HDA [auth B5],
HE [auth B1],
HEA [auth B5],
HF [auth B1],
HFA [auth L5],
HG [auth J1],
HH [auth A2],
HI [auth A2],
HJ [auth B2],
HK [auth B2],
HM [auth A3],
HN [auth A3],
HO [auth B3],
HP [auth B3],
HR [auth A4],
HS [auth A4],
HT [auth B4],
HU [auth B4],
HV [auth K4],
HW [auth A6],
HX [auth A6],
HY [auth B6],
HZ [auth B6],
IBA [auth A5],
IC [auth A1],
ID [auth A1],
IDA [auth B5],
IE [auth B1],
IEA [auth B5],
IF [auth B1],
IFA [auth L5],
IG [auth J1],
IH [auth A2],
II [auth A2],
IJ [auth B2],
IK [auth B2],
IM [auth A3],
IN [auth A3],
IO [auth B3],
IP [auth B3],
IR [auth A4],
IS [auth A4],
IT [auth B4],
IU [auth B4],
IV [auth L4],
IW [auth A6],
IY [auth B6],
JAA [auth L6],
JBA [auth A5],
JC [auth A1],
JD [auth A1],
JDA [auth B5],
JE [auth B1],
JF [auth B1],
JFA [auth L5],
JH [auth A2],
JI [auth A2],
JJ [auth B2],
JK [auth B2],
JL [auth K2],
JM [auth A3],
JN [auth A3],
JO [auth B3],
JP [auth B3],
JQ [auth K3],
JR [auth A4],
JS [auth A4],
JT [auth B4],
JU [auth B4],
JW [auth A6],
JY [auth B6],
KAA [auth L6],
KBA [auth A5],
KC [auth A1],
KD [auth A1],
KDA [auth B5],
KE [auth B1],
KF [auth B1],
KH [auth A2],
KI [auth A2],
KJ [auth B2],
KK [auth B2],
KM [auth A3],
KN [auth A3],
KO [auth B3],
KP [auth B3],
KR [auth A4],
KT [auth B4],
KU [auth B4],
KV [auth L4],
KW [auth A6],
KY [auth B6],
LAA [auth L6],
LBA [auth A5],
LC [auth A1],
LD [auth A1],
LDA [auth B5],
LE [auth B1],
LF [auth B1],
LG [auth K1],
LH [auth A2],
LI [auth A2],
LJ [auth B2],
LK [auth B2],
LL [auth L2],
LM [auth A3],
LN [auth A3],
LO [auth B3],
LP [auth B3],
LQ [auth L3],
LR [auth A4],
LT [auth B4],
LU [auth B4],
LV [auth L4],
LW [auth A6],
LY [auth B6],
MBA [auth A5],
MC [auth A1],
MD [auth A1],
MDA [auth B5],
ME [auth B1],
MF [auth B1],
MFA [auth X5],
MG [auth L1],
MH [auth A2],
MI [auth A2],
MJ [auth B2],
MK [auth B2],
MM [auth A3],
MN [auth A3],
MO [auth B3],
MP [auth B3],
MQ [auth L3],
MR [auth A4],
MT [auth B4],
MV [auth L4],
MW [auth A6],
MY [auth B6],
NAA [auth M6],
NBA [auth A5],
NC [auth A1],
ND [auth A1],
NDA [auth B5],
NE [auth B1],
NG [auth L1],
NH [auth A2],
NI [auth A2],
NJ [auth B2],
NK [auth B2],
NM [auth A3],
NN [auth A3],
NO [auth B3],
NP [auth B3],
NQ [auth L3],
NR [auth A4],
NT [auth B4],
NW [auth A6],
NY [auth B6],
OBA [auth A5],
OC [auth A1],
ODA [auth B5],
OE [auth B1],
OH [auth A2],
OI [auth A2],
OJ [auth B2],
OK [auth B2],
OL [auth L2],
OM [auth A3],
OO [auth B3],
OP [auth B3],
OQ [auth L3],
OR [auth A4],
OT [auth B4],
OW [auth A6],
OY [auth B6],
PAA [auth X6],
PBA [auth A5],
PC [auth A1],
PDA [auth B5],
PE [auth B1],
PH [auth A2],
PI [auth A2],
PJ [auth B2],
PL [auth L2],
PM [auth A3],
PO [auth B3],
PP [auth B3],
PR [auth A4],
PT [auth B4],
PW [auth A6],
PY [auth B6],
QAA [auth A5],
QBA [auth A5],
QC [auth A1],
QDA [auth B5],
QE [auth B1],
QG [auth L1],
QH [auth A2],
QI [auth A2],
QJ [auth B2],
QL [auth L2],
QM [auth A3],
QO [auth B3],
QQ [auth M3],
QR [auth A4],
QT [auth B4],
QW [auth A6],
QY [auth B6],
RAA [auth A5],
RBA [auth A5],
RC [auth A1],
RDA [auth B5],
RE [auth B1],
RG [auth L1],
RH [auth A2],
RJ [auth B2],
RM [auth A3],
RO [auth B3],
RR [auth A4],
RT [auth B4],
RW [auth A6],
RX [auth A6],
RY [auth B6],
SAA [auth A5],
SBA [auth A5],
SC [auth A1],
SCA [auth B5],
SDA [auth B5],
SE [auth B1],
SG [auth L1],
SH [auth A2],
SJ [auth B2],
SL [auth M2],
SM [auth A3],
SO [auth B3],
SR [auth A4],
ST [auth B4],
SV [auth X4],
SW [auth A6],
SY [auth B6],
TAA [auth A5],
TBA [auth A5],
TC [auth A1],
TCA [auth B5],
TDA [auth B5],
TE [auth B1],
TEA [auth F5],
TH [auth A2],
TJ [auth B2],
TM [auth A3],
TO [auth B3],
TQ [auth X3],
TR [auth A4],
TT [auth B4],
TV [auth A6],
TW [auth A6],
TY [auth B6],
UAA [auth A5],
UBA [auth A5],
UC [auth A1],
UCA [auth B5],
UDA [auth B5],
UE [auth B1],
UH [auth A2],
UJ [auth B2],
UL [auth X2],
UM [auth A3],
UO [auth B3],
UQ [auth A4],
UR [auth A4],
US [auth A4],
UT [auth B4],
UU [auth B4],
UV [auth A6],
UW [auth A6],
UX [auth B6],
UY [auth B6],
UZ [auth F6],
VAA [auth A5],
VBA [auth A5],
VC [auth A1],
VCA [auth B5],
VDA [auth B5],
VE [auth B1],
VG [auth M1],
VH [auth A2],
VJ [auth B2],
VL [auth A3],
VM [auth A3],
VO [auth B3],
VQ [auth A4],
VR [auth A4],
VS [auth B4],
VT [auth B4],
VV [auth A6],
VW [auth A6],
VX [auth B6],
VY [auth B6],
WAA [auth A5],
WBA [auth A5],
WC [auth A1],
WCA [auth B5],
WDA [auth B5],
WE [auth B1],
WH [auth A2],
WJ [auth B2],
WL [auth A3],
WM [auth A3],
WO [auth B3],
WQ [auth A4],
WR [auth A4],
WS [auth B4],
WT [auth B4],
WV [auth A6],
WW [auth A6],
WX [auth B6],
WY [auth B6],
WZ [auth I6],
XAA [auth A5],
XBA [auth A5],
XC [auth A1],
XCA [auth B5],
XDA [auth B5],
XE [auth B1],
XEA [auth J5],
XG [auth X1],
XH [auth A2],
XJ [auth B2],
XL [auth A3],
XM [auth A3],
XO [auth B3],
XQ [auth A4],
XR [auth A4],
XS [auth B4],
XT [auth B4],
XV [auth A6],
XW [auth A6],
XX [auth B6],
XY [auth B6],
YAA [auth A5],
YBA [auth A5],
YC [auth A1],
YCA [auth B5],
YD [auth B1],
YDA [auth B5],
YE [auth B1],
YEA [auth J5],
YF [auth B1],
YG [auth A2],
YH [auth A2],
YJ [auth B2],
YL [auth A3],
YM [auth A3],
YO [auth B3],
YQ [auth A4],
YR [auth A4],
YS [auth B4],
YT [auth B4],
YU [auth F4],
YV [auth A6],
YW [auth A6],
YX [auth B6],
YY [auth B6],
YZ [auth J6],
ZAA [auth A5],
ZBA [auth A5],
ZC [auth A1],
ZCA [auth B5],
ZD [auth B1],
ZDA [auth B5],
ZE [auth B1],
ZF [auth B1],
ZG [auth A2],
ZH [auth A2],
ZJ [auth B2],
ZL [auth A3],
ZM [auth A3],
ZN [auth B3],
ZO [auth B3],
ZQ [auth A4],
ZR [auth A4],
ZS [auth B4],
ZT [auth B4],
ZV [auth A6],
ZW [auth A6],
ZX [auth B6],
ZY [auth B6],
ZZ [auth J6]
CHLOROPHYLL A
C55 H72 Mg N4 O5
ATNHDLDRLWWWCB-AENOIHSZSA-M
LMG
Query on LMG
Download Ideal Coordinates CCD File 
OZ [auth B6]
QEA [auth B5]
TU [auth B4]
VF [auth B1]
WK [auth B2]
OZ [auth B6],
QEA [auth B5],
TU [auth B4],
VF [auth B1],
WK [auth B2],
WP [auth B3]
1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE
C45 H86 O10
DCLTVZLYPPIIID-CVELTQQQSA-N
LHG
Query on LHG
Download Ideal Coordinates CCD File 
NFA [auth X5]
OCA [auth A5]
PCA [auth A5]
PX [auth A6]
PZ [auth B6]
NFA [auth X5],
OCA [auth A5],
PCA [auth A5],
PX [auth A6],
PZ [auth B6],
QX [auth A6],
RS [auth A4],
RV [auth X4],
SQ [auth X3],
SS [auth A4],
VD [auth A1],
VN [auth A3],
WD [auth A1],
WF [auth B1],
WN [auth A3],
XK [auth B2],
YI [auth A2],
ZI [auth A2]
1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE
C38 H75 O10 P
BIABMEZBCHDPBV-MPQUPPDSSA-N
BCR
Query on BCR
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AFA [auth J5]
AQ [auth F3]
AV [auth F4]
BAA [auth J6]
BFA [auth J5]
AFA [auth J5],
AQ [auth F3],
AV [auth F4],
BAA [auth J6],
BFA [auth J5],
BL [auth F2],
BV [auth I4],
CAA [auth J6],
CQ [auth F3],
CV [auth I4],
DG [auth F1],
DL [auth F2],
DQ [auth I3],
EAA [auth L6],
EFA [auth L5],
EQ [auth I3],
FG [auth I1],
FL [auth I2],
FV [auth J4],
GG [auth I1],
GV [auth J4],
HAA [auth L6],
HL [auth J2],
HQ [auth J3],
ICA [auth A5],
IL [auth J2],
IQ [auth J3],
JCA [auth A5],
JG [auth J1],
JX [auth A6],
JZ [auth B6],
KCA [auth A5],
KEA [auth B5],
KFA [auth L5],
KG [auth J1],
KL [auth L2],
KQ [auth L3],
KX [auth A6],
KZ [auth B6],
LCA [auth A5],
LEA [auth B5],
LFA [auth M5],
LS [auth A4],
LX [auth A6],
LZ [auth B6],
MAA [auth L6],
MCA [auth A5],
MEA [auth B5],
ML [auth L2],
MS [auth A4],
MX [auth A6],
MZ [auth B6],
NCA [auth A5],
NEA [auth B5],
NS [auth A4],
NU [auth B4],
NV [auth L4],
NX [auth A6],
NZ [auth B6],
OAA [auth M6],
OEA [auth B5],
OF [auth B1],
OG [auth L1],
OS [auth A4],
OU [auth B4],
OX [auth A6],
PD [auth A1],
PEA [auth B5],
PF [auth B1],
PN [auth A3],
PQ [auth L3],
PS [auth A4],
PU [auth B4],
PV [auth L4],
QCA [auth A5],
QD [auth A1],
QF [auth B1],
QK [auth B2],
QN [auth A3],
QS [auth A4],
QU [auth B4],
QV [auth M4],
QZ [auth B6],
RD [auth A1],
RF [auth B1],
RK [auth B2],
RL [auth L2],
RN [auth A3],
RP [auth B3],
RQ [auth M3],
RU [auth B4],
SD [auth A1],
SF [auth B1],
SI [auth A2],
SK [auth B2],
SN [auth A3],
SP [auth B3],
SU [auth B4],
SX [auth A6],
TD [auth A1],
TF [auth B1],
TI [auth A2],
TK [auth B2],
TL [auth M2],
TN [auth A3],
TP [auth B3],
TZ [auth F6],
UD [auth A1],
UEA [auth F5],
UF [auth B1],
UG [auth L1],
UI [auth A2],
UK [auth B2],
UN [auth A3],
UP [auth B3],
VEA [auth I5],
VI [auth A2],
VK [auth B2],
VP [auth B3],
VZ [auth F6],
WEA [auth I5],
WG [auth M1],
WI [auth A2],
XF [auth B1],
XI [auth A2],
XP [auth B3],
XU [auth F4],
XZ [auth I6],
YK [auth B2],
YN [auth A3],
ZEA [auth J5],
ZU [auth F4]
BETA-CAROTENE
C40 H56
OENHQHLEOONYIE-JLTXGRSLSA-N
PQN
Query on PQN
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HCA [auth A5]
IX [auth A6]
IZ [auth B6]
JEA [auth B5]
KS [auth A4]
HCA [auth A5],
IX [auth A6],
IZ [auth B6],
JEA [auth B5],
KS [auth A4],
MU [auth B4],
NF [auth B1],
OD [auth A1],
ON [auth A3],
PK [auth B2],
QP [auth B3],
RI [auth A2]
PHYLLOQUINONE
C31 H46 O2
MBWXNTAXLNYFJB-NKFFZRIASA-N
SF4
Query on SF4
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AG [auth C1]
AJ [auth A2]
AL [auth C2]
BG [auth C1]
RCA [auth A5]
AG [auth C1],
AJ [auth A2],
AL [auth C2],
BG [auth C1],
RCA [auth A5],
REA [auth C5],
RZ [auth C6],
SEA [auth C5],
SZ [auth C6],
TS [auth A4],
TX [auth B6],
VU [auth C4],
WU [auth C4],
XD [auth A1],
XN [auth A3],
YP [auth C3],
ZK [auth C2],
ZP [auth C3]
IRON/SULFUR CLUSTER
Fe4 S4
LJBDFODJNLIPKO-UHFFFAOYSA-N
FES
Query on FES
Download Ideal Coordinates CCD File 
OFA [auth P1]
PFA [auth P2]
QFA [auth P3]
RFA [auth P4]
SFA [auth P6]
OFA [auth P1],
PFA [auth P2],
QFA [auth P3],
RFA [auth P4],
SFA [auth P6],
TFA [auth P5]
FE2/S2 (INORGANIC) CLUSTER
Fe2 S2
NIXDOXVAJZFRNF-UHFFFAOYSA-N
CA
Query on CA
Download Ideal Coordinates CCD File 
IAA [auth L6]
JV [auth L4]
NL [auth L2]
OV [auth L4]
PG [auth L1]
IAA [auth L6],
JV [auth L4],
NL [auth L2],
OV [auth L4],
PG [auth L1],
TG [auth L1]
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 4.20 Å
  • R-Value Free: 0.377 
  • R-Value Work: 0.353 
  • R-Value Observed: 0.354 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 214.101α = 90
b = 239.668β = 101.08
c = 265.605γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
iMOSFLMdata reduction
SCALAdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


View more in-depth experimental data
Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
Japan Society for the Promotion of ScienceJapanGS016
Japan science and technology agencyJapan--
Japan Society for the Promotion of ScienceJapan13J03550

Revision History  (Full details and data files)

  • Version 1.0: 2018-04-11
    Type: Initial release
  • Version 1.1: 2018-04-25
    Changes: Data collection, Database references
  • Version 2.0: 2023-11-22
    Changes: Data collection, Database references, Derived calculations, Non-polymer description, Refinement description
  • Version 2.1: 2024-10-23
    Changes: Structure summary