2VML | pdb_00002vml

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 (Depositor), 0.220 (DCC)
R-Value Work:
0.192 (Depositor), 0.190 (DCC)
R-Value Observed:
0.194 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.4 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
Modeled Residue Count: 2,004
Deposited Residue Count: 2,004
Unique protein chains: 2

Macromolecules

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(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

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(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 AA [auth J] SDF format, chain BA [auth K] SDF format, chain CA [auth L] SDF format, chain DA [auth L] SDF format, chain M [auth A] SDF format, chain O [auth B] SDF format, chain P [auth C] 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 W [auth H] SDF format, chain X [auth H] SDF format, chain Z [auth J] SDF format, chain Y [auth I] SDF format, chain T [auth F] SDF format, chain R [auth D] SDF format, chain N [auth B] MOL2 format, chain AA [auth J] MOL2 format, chain BA [auth K] MOL2 format, chain CA [auth L] MOL2 format, chain DA [auth L] MOL2 format, chain M [auth A] MOL2 format, chain O [auth B] MOL2 format, chain P [auth C] 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 W [auth H] MOL2 format, chain X [auth H] MOL2 format, chain Z [auth J] MOL2 format, chain Y [auth I] MOL2 format, chain T [auth F] MOL2 format, chain R [auth D] MOL2 format, chain N [auth B] mmCIF format, chain AA [auth J] mmCIF format, chain BA [auth K] mmCIF format, chain CA [auth L] mmCIF format, chain DA [auth L] mmCIF format, chain M [auth A] mmCIF format, chain O [auth B] mmCIF format, chain P [auth C] mmCIF format, chain Q [auth D] mmCIF format, chain S [auth E] mmCIF format, chain U [auth F] mmCIF format, chain V [auth G] mmCIF format, chain W [auth H] mmCIF format, chain X [auth H] mmCIF format, chain Z [auth J] mmCIF format, chain Y [auth I] mmCIF format, chain T [auth F] mmCIF format, chain R [auth D] mmCIF format, chain N [auth B]	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 (Depositor), 0.220 (DCC)
R-Value Work: 0.192 (Depositor), 0.190 (DCC)
R-Value Observed: 0.194 (Depositor)

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

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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
Version 1.4: 2024-11-06
Changes: Structure summary