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

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.3 of the entry. See complete history.

Literature

The Structures of the Phycobiliproteins of Gloeobacter Violaceus

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

To be published.

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

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
PHYCOCYANIN ALPHA CHAIN	A, C, E, G, I 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 Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q7M7F7
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
PHYCOCYANIN BETA CHAIN	B, D, F, H, J 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
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q7M7C7
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
CYC Query on CYC Download Ideal Coordinates CCD File SDF format, chain CA [auth L] SDF format, chain M [auth A] SDF format, chain N [auth B] SDF format, chain Q [auth D] SDF format, chain S [auth E] SDF format, chain U [auth F] SDF format, chain V [auth G] SDF format, chain AA [auth J] SDF format, chain BA [auth K] SDF format, chain DA [auth L] SDF format, chain O [auth B] SDF format, chain P [auth C] SDF format, chain R [auth D] SDF format, chain T [auth F] SDF format, chain W [auth H] SDF format, chain X [auth H] SDF format, chain Y [auth I] SDF format, chain Z [auth J] MOL2 format, chain CA [auth L] MOL2 format, chain M [auth A] MOL2 format, chain N [auth B] MOL2 format, chain Q [auth D] MOL2 format, chain S [auth E] MOL2 format, chain U [auth F] MOL2 format, chain V [auth G] MOL2 format, chain AA [auth J] MOL2 format, chain BA [auth K] MOL2 format, chain DA [auth L] MOL2 format, chain O [auth B] MOL2 format, chain P [auth C] MOL2 format, chain R [auth D] MOL2 format, chain T [auth F] MOL2 format, chain W [auth H] MOL2 format, chain X [auth H] MOL2 format, chain Y [auth I] MOL2 format, chain Z [auth J]	AA [auth J] BA [auth K] CA [auth L] DA [auth L] M [auth A] 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		Interactions Focus chain AA [auth J] Focus chain BA [auth K] Focus chain CA [auth L] Focus chain DA [auth L] Focus chain M [auth A] Focus chain N [auth B] Focus chain O [auth B] Focus chain P [auth C] Focus chain Q [auth D] Focus chain R [auth D] Focus chain S [auth E] Focus chain T [auth F] Focus chain U [auth F] Focus chain V [auth G] Focus chain W [auth H] Focus chain X [auth H] Focus chain Y [auth I] Focus chain Z [auth J] Interactions & Density Focus chain AA [auth J] Focus chain BA [auth K] Focus chain CA [auth L] Focus chain DA [auth L] Focus chain M [auth A] Focus chain N [auth B] Focus chain O [auth B] Focus chain P [auth C] Focus chain Q [auth D] Focus chain R [auth D] Focus chain S [auth E] Focus chain T [auth F] Focus chain U [auth F] Focus chain V [auth G] Focus chain W [auth H] Focus chain X [auth H] Focus chain Y [auth I] Focus chain Z [auth J]

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

View Full Validation Report

Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2008-03-25

Deposition Author(s):

Murray, J.W.

Benson, S.

Barber, J.

Revision History (Full details and data files)

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

Prepare Data

Validate Data

Deposit Data

Help and Resources

2VML

The monoclinic structure of phycocyanin from Gloeobacter violaceus

The Structures of the Phycobiliproteins of Gloeobacter Violaceus

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

Expand

Entity ID: 2