4XKB

Crystal Structure of GENOMES UNCOUPLED 4 (GUN4) in Complex with Deuteroporphyrin IX

PDB DOI: https://doi.org/10.2210/pdb4XKB/pdb

Classification: LIGAND BINDING PROTEIN
Organism(s): Synechocystis sp. PCC 6803 substr. Kazusa
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2015-01-11 Released: 2015-05-20
Deposition Author(s): Chen, X., Pu, H., Liu, L.
Funding Organization(s): Chinese Academy of Sciences

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.50 Å
R-Value Free: 0.196
R-Value Work: 0.160
R-Value Observed: 0.162

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Crystal Structures of GUN4 in Complex with Porphyrins.

Chen, X., Pu, H., Wang, X., Long, W., Lin, R., Liu, L.

(2015) Mol Plant 8: 1125-1127

PubMed: 25958236 Search on PubMed
DOI: https://doi.org/10.1016/j.molp.2015.04.013
Primary Citation of Related Structures:
4XKB, 4XKC

Organizational Affiliation

Photosynthesis Research Center, Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of Sciences, 20 Nanxincun, Haidian District, Beijing 100093, China; University of Chinese Academy of Sciences, 19A Yuquan Road, Haidian District, Beijing 100049, China.

Macromolecule Content

Total Structure Weight: 27 kDa
Atom Count: 2,221
Modelled Residue Count: 225
Deposited Residue Count: 233
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Ycf53-like protein	A	233	Synechocystis sp. PCC 6803 substr. Kazusa	Mutation(s): 0 Gene Names: sll0558
UniProt
Find proteins for P72583 (Synechocystis sp. (strain ATCC 27184 / PCC 6803 / Kazusa)) Explore P72583 Go to UniProtKB: P72583
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P72583
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
DE9 Query on DE9 Download Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	3,3'-(3,7,12,17-tetramethylporphyrin-2,18-diyl)dipropanoic acid C₃₀ H₃₀ N₄ O₄ VVNYLNWIIBXFLK-LMKUSPAJSA-N		Interactions Focus chain B [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.50 Å
R-Value Free: 0.196
R-Value Work: 0.160
R-Value Observed: 0.162
Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 32.792	α = 90
b = 64.01	β = 90
c = 105.432	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHASER	phasing
PHENIX	refinement

Structure Validation

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Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2015-05-20

Deposition Author(s):

Chen, X.

Pu, H.

Liu, L.

Funding Organization	Location	Grant Number
Chinese Academy of Sciences	China	2011CBA00901

Revision History (Full details and data files)

Version 1.0: 2015-05-20
Type: Initial release
Version 1.1: 2015-07-15
Changes: Database references
Version 1.2: 2015-07-22
Changes: Database references
Version 1.3: 2023-11-08
Changes: Data collection, Database references, Derived calculations, Refinement description, Source and taxonomy