2VML

The monoclinic structure of phycocyanin from Gloeobacter violaceus

• PDB DOI: https://doi.org/10.2210/pdb2VML/pdb

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


• Deposited: 2008-01-28 Released: 2008-03-25 
• Deposition Author(s): Murray, J.W., Benson, S., Barber, J.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free: 0.218 
• R-Value Work: 0.192 
• R-Value Observed: 0.194 

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 assigned by authors and generated by PQS (software)

Macromolecule Content

• Total Structure Weight: 227.55 kDa 
• Atom Count: 16,700 
• Modelled Residue Count: 2,004 
• Deposited Residue Count: 2,004 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
PHYCOCYANIN ALPHA CHAIN	A, C, E, G, I, K	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, D, F, H, J, L	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	AA [auth J], BA [auth K], CA [auth L], DA [auth L], M [auth A], N [auth B], O [auth B], P [auth C], Q [auth D], R [auth D], S [auth E], T [auth F], U [auth F], V [auth G], W [auth H], X [auth H], Y [auth I], Z [auth J]	PHYCOCYANOBILIN C33 H40 N4 O6 VXTXPYZGDQPMHK-GMXXPEQVSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free: 0.218 
• R-Value Work: 0.192 
• R-Value Observed: 0.194 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 86.877	α = 90
b = 142.04	β = 107.65
c = 115.313	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2008-03-25 
Deposition Author(s): Murray, J.W., Benson, S., 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, Derived calculations, Other, Refinement description