2VJR | pdb_00002vjr

The structure of phycocyanin from Gloeobacter violaceus

• PDB DOI: https://doi.org/10.2210/pdb2VJR/pdb

• Classification: PHOTOSYNTHESIS
• Organism(s): Gloeobacter violaceus
• Mutation(s): No 


• Deposited: 2007-12-12 Released: 2008-03-25 
• Deposition Author(s): Murray, J.W., Benson, S., Nield, J., Barber, J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free: 
  0.266 (Depositor), 0.256 (DCC) 
• R-Value Work: 
  0.207 (Depositor), 0.206 (DCC) 
• R-Value Observed: 
  0.210 (Depositor) 

Starting Model: experimental

Literature

The Structures of the Phycobiliproteins of Gloeobacter Violaceus

Murray, J.W., Benson, S., Nield, J., Barber, J.

To be published.

Biological Assembly 1  

Global Symmetry: Dihedral - D3  (Explore in 3D)
Global Stoichiometry: Hetero 12-mer - A6B6 Pseudo Symmetry: Dihedral - D3  (Explore in 3D)
Pseudo Stoichiometry: Homo 12-mer - A12 

Biological assembly 1 generated by PQS (software)

Macromolecule Content 

• Total Structure Weight: 37.92 kDa 
• Atom Count: 2,749 
• Modeled Residue Count: 334 
• Deposited Residue Count: 334 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
PHYCOCYANIN ALPHA CHAIN	A	162	Gloeobacter violaceus	Mutation(s): 0
UniProt
Find proteins for Q7M7F7 (Gloeobacter violaceus (strain ATCC 29082 / PCC 7421)) Explore Q7M7F7  Go to UniProtKB:  Q7M7F7

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
PHYCOCYANIN BETA CHAIN	B	172	Gloeobacter violaceus	Mutation(s): 0
UniProt
Find proteins for Q7M7C7 (Gloeobacter violaceus (strain ATCC 29082 / PCC 7421)) Explore Q7M7C7  Go to UniProtKB:  Q7M7C7

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CYC	C [auth A], D [auth B], E [auth B]	PHYCOCYANOBILIN C33 H40 N4 O6 VXTXPYZGDQPMHK-GMXXPEQVSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free:  0.266 (Depositor), 0.256 (DCC) 
• R-Value Work:  0.207 (Depositor), 0.206 (DCC) 
• R-Value Observed: 0.210 (Depositor) 

Space Group: P 6₃ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 117.538	α = 90
b = 117.538	β = 90
c = 116.163	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2008-03-25 
Deposition Author(s): Murray, J.W., Benson, S., Nield, J., Barber, J.

Revision History  

• Version 1.0: 2008-03-25
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Advisory, Refinement description, Version format compliance
• Version 1.2: 2019-05-08
  Changes: Data collection, Derived calculations, Experimental preparation, Other
• Version 1.3: 2023-12-13
  Changes: Data collection, Database references, Other, Refinement description
• Version 1.4: 2024-11-13
  Changes: Structure summary