6YX7

The high resolution structure of allophycocyanin from cyanobacterium Nostoc sp. WR13, the P21212 crystal form.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.42 Å
  • R-Value Free: 0.175 
  • R-Value Work: 0.126 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

The high resolution structure of allophycocyanin from cyanobacterium Nostoc sp. WR13

Patel, H.M.Roszak, A.W.Madamwar, D.Cogdell, R.J.

To be published.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Allophycocyanin alpha160Nostoc sp. WR13Mutation(s): 0 
UniProt
Find proteins for A0A4Y5PW22 (Nostoc sp. WR13)
Explore A0A4Y5PW22 
Go to UniProtKB:  A0A4Y5PW22
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A4Y5PW22
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Allophycocyanin beta161Nostoc sp. WR13Mutation(s): 0 
UniProt
Find proteins for A0A4Y5PW23 (Nostoc sp. WR13)
Explore A0A4Y5PW23 
Go to UniProtKB:  A0A4Y5PW23
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A4Y5PW23
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 14 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
CYC (Subject of Investigation/LOI)
Query on CYC

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CA [auth DDD]
CB [auth KKK]
FA [auth EEE]
GB [auth LLL]
IA [auth FFF]
CA [auth DDD],
CB [auth KKK],
FA [auth EEE],
GB [auth LLL],
IA [auth FFF],
M [auth AAA],
MA [auth GGG],
O [auth BBB],
RA [auth HHH],
VA [auth III],
W [auth CCC],
XA [auth JJJ]
PHYCOCYANOBILIN
C33 H40 N4 O6
VXTXPYZGDQPMHK-GMXXPEQVSA-N
P6G
Query on P6G

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X [auth CCC]HEXAETHYLENE GLYCOL
C12 H26 O7
IIRDTKBZINWQAW-UHFFFAOYSA-N
1PE
Query on 1PE

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R [auth BBB]PENTAETHYLENE GLYCOL
C10 H22 O6
JLFNLZLINWHATN-UHFFFAOYSA-N
PG4
Query on PG4

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AB [auth JJJ],
LA [auth FFF],
N [auth AAA],
Y [auth CCC]
TETRAETHYLENE GLYCOL
C8 H18 O5
UWHCKJMYHZGTIT-UHFFFAOYSA-N
PGE
Query on PGE

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JB [auth LLL],
OA [auth GGG],
PA [auth GGG]
TRIETHYLENE GLYCOL
C6 H14 O4
ZIBGPFATKBEMQZ-UHFFFAOYSA-N
LYS
Query on LYS

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DB [auth KKK],
P [auth BBB],
WA [auth III]
LYSINE
C6 H15 N2 O2
KDXKERNSBIXSRK-YFKPBYRVSA-O
GLU
Query on GLU

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DA [auth DDD],
SA [auth HHH]
GLUTAMIC ACID
C5 H9 N O4
WHUUTDBJXJRKMK-VKHMYHEASA-N
MRD
Query on MRD

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NA [auth GGG](4R)-2-METHYLPENTANE-2,4-DIOL
C6 H14 O2
SVTBMSDMJJWYQN-RXMQYKEDSA-N
MPD
Query on MPD

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EA [auth DDD]
HA [auth EEE]
IB [auth LLL]
KA [auth FFF]
Q [auth BBB]
EA [auth DDD],
HA [auth EEE],
IB [auth LLL],
KA [auth FFF],
Q [auth BBB],
TA [auth HHH],
ZA [auth JJJ]
(4S)-2-METHYL-2,4-PENTANEDIOL
C6 H14 O2
SVTBMSDMJJWYQN-YFKPBYRVSA-N
PEG
Query on PEG

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BB [auth JJJ]
QA [auth GGG]
S [auth BBB]
T [auth BBB]
UA [auth HHH]
BB [auth JJJ],
QA [auth GGG],
S [auth BBB],
T [auth BBB],
UA [auth HHH],
V [auth BBB],
Z [auth CCC]
DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
DSN
Query on DSN

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HB [auth LLL],
YA [auth JJJ]
D-SERINE
C3 H7 N O3
MTCFGRXMJLQNBG-UWTATZPHSA-N
ALA
Query on ALA

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JA [auth FFF]ALANINE
C3 H7 N O2
QNAYBMKLOCPYGJ-REOHCLBHSA-N
GLY
Query on GLY

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GA [auth EEE]GLYCINE
C2 H5 N O2
DHMQDGOQFOQNFH-UHFFFAOYSA-N
EDO
Query on EDO

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AA [auth CCC],
BA [auth CCC],
EB [auth KKK],
FB [auth KKK],
U [auth BBB]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
MEN
Query on MEN
B [auth BBB]
D [auth DDD]
F [auth FFF]
H [auth HHH]
J [auth JJJ]
B [auth BBB],
D [auth DDD],
F [auth FFF],
H [auth HHH],
J [auth JJJ],
L [auth LLL]
L-PEPTIDE LINKINGC5 H10 N2 O3ASN
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.42 Å
  • R-Value Free: 0.175 
  • R-Value Work: 0.126 
  • Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 123.695α = 90
b = 177.726β = 90
c = 106.372γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
autoPROCdata scaling
STARANISOdata scaling
PHASERphasing
Cootmodel building

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Department of Energy (DOE, United States)United StatesDE-SC0001035 (Office of Basic Energy Sciences)
Department of Biotechnology (DBT, India)IndiaBT/PR15686/AAQ/3/811/2016 (UGC-BSR Faculty Fellowship)
Department of Biotechnology (DBT, India)IndiaBT/IN/UK/DBT-BC/2017-18 (Newton-Bhabha fellowship)

Revision History  (Full details and data files)

  • Version 1.0: 2021-05-12
    Type: Initial release
  • Version 1.1: 2024-01-24
    Changes: Data collection, Database references, Derived calculations, Refinement description