2VJH | pdb_00002vjh

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.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.20 Å
R-Value Free:
0.186 (Depositor), 0.160 (DCC)
R-Value Work:
0.153 (Depositor), 0.162 (DCC)
R-Value Observed:
0.155 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.2 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: 78.17 kDa
Atom Count: 6,116
Modeled Residue Count: 682
Deposited Residue Count: 682
Unique protein chains: 2

Macromolecules

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| 3D Structure

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 Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q7NLD7
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

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
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q7NLD6
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PUB Query on PUB Download:Ideal Coordinates CCD File SDF format, chain L [auth D] SDF format, chain G [auth B] MOL2 format, chain L [auth D] MOL2 format, chain G [auth B] mmCIF format, chain L [auth D] mmCIF format, chain G [auth B]	G [auth B], L [auth D]	PHYCOUROBILIN C₃₃ H₄₂ N₄ O₆ KDCCOOGTVSRCHX-YYVBKQGDSA-N		Interactions Focus chain G [auth B] Focus chain L [auth D] Interactions & Density Focus chain G [auth B] Focus chain L [auth D]
PEB Query on PEB Download:Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain F [auth A] SDF format, chain H [auth B] SDF format, chain I [auth B] SDF format, chain J [auth C] SDF format, chain K [auth C] SDF format, chain M [auth D] SDF format, chain N [auth D] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain H [auth B] MOL2 format, chain I [auth B] MOL2 format, chain J [auth C] MOL2 format, chain K [auth C] MOL2 format, chain M [auth D] MOL2 format, chain N [auth D] mmCIF format, chain E [auth A] mmCIF format, chain F [auth A] mmCIF format, chain H [auth B] mmCIF format, chain I [auth B] mmCIF format, chain J [auth C] mmCIF format, chain K [auth C] mmCIF format, chain M [auth D] mmCIF format, chain N [auth D]	E [auth A] F [auth A] H [auth B] I [auth B] J [auth C] 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		Interactions Focus chain E [auth A] Focus chain F [auth A] Focus chain H [auth B] Focus chain I [auth B] Focus chain J [auth C] Focus chain K [auth C] Focus chain M [auth D] Focus chain N [auth D] Interactions & Density Focus chain E [auth A] Focus chain F [auth A] Focus chain H [auth B] Focus chain I [auth B] Focus chain J [auth C] Focus chain K [auth C] Focus chain M [auth D] Focus chain N [auth D]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MEN Query on 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 (Depositor), 0.160 (DCC)
R-Value Work: 0.153 (Depositor), 0.162 (DCC)
R-Value Observed: 0.155 (Depositor)

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

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2008-03-25

Deposition Author(s):

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