2VJH

The structure of Phycoerythrin from Gloeobacter violaceus

• PDB DOI: https://doi.org/10.2210/pdb2VJH/pdb

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


• Deposited: 2007-12-10 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: 2.20 Å
• R-Value Free: 0.186 
• R-Value Work: 0.153 
• R-Value Observed: 0.155 

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: 78.17 kDa 
• Atom Count: 6,116 
• Modelled Residue Count: 682 
• Deposited Residue Count: 682 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
PHYCOERYTHRIN ALPHA CHAIN	A, C	164	Gloeobacter violaceus	Mutation(s): 0
UniProt
Find proteins for Q7NLD7 (Gloeobacter violaceus (strain ATCC 29082 / PCC 7421)) Explore Q7NLD7  Go to UniProtKB:  Q7NLD7

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
PHYCOERYTHRIN BETA SUBUNIT	B, D	177	Gloeobacter violaceus	Mutation(s): 0
UniProt
Find proteins for Q7NLD6 (Gloeobacter violaceus (strain ATCC 29082 / PCC 7421)) Explore Q7NLD6  Go to UniProtKB:  Q7NLD6

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PUB	G [auth B], L [auth D]	PHYCOUROBILIN C33 H42 N4 O6 KDCCOOGTVSRCHX-YYVBKQGDSA-N
PEB	E [auth A], F [auth A], H [auth B], I [auth B], J [auth C], K [auth C], M [auth D], N [auth D]	PHYCOERYTHROBILIN C33 H40 N4 O6 NKCBCVIFPXGHAV-WAVSMFBNSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MEN	B, D	L-PEPTIDE LINKING	C5 H10 N2 O3		ASN

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 0.186 
• R-Value Work: 0.153 
• R-Value Observed: 0.155 
• Space Group: P 2₁ 3

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 155.829	α = 90
b = 155.829	β = 90
c = 155.829	γ = 90

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: 2023-12-13
  Changes: Data collection, Database references, Derived calculations, Other, Refinement description