4XKB | pdb_00004xkb

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

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.50 Å
• R-Value Free: 
  0.196 (Depositor), 0.196 (DCC) 
• R-Value Work: 
  0.160 (Depositor), 0.162 (DCC) 
• R-Value Observed: 
  0.162 (Depositor) 

Starting Model: experimental

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 
• DOI: https://doi.org/10.1016/j.molp.2015.04.013
• Primary Citation Related Structures: 
  4XKB, 4XKC

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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.
Photosynthesis Research Center, Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of Sciences, 20 Nanxincun, Haidian District, Beijing 100093, China.
Photosynthesis Research Center, Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of Sciences, 20 Nanxincun, Haidian District, Beijing 100093, China. Electronic address: [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Macromolecule Content 

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

Macromolecules

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

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
DE9	B [auth A]	3,3'-(3,7,12,17-tetramethylporphyrin-2,18-diyl)dipropanoic acid C30 H30 N4 O4 VVNYLNWIIBXFLK-LMKUSPAJSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.50 Å
• R-Value Free:  0.196 (Depositor), 0.196 (DCC) 
• R-Value Work:  0.160 (Depositor), 0.162 (DCC) 
• R-Value Observed: 0.162 (Depositor) 

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

Entry History 

& Funding Information

Deposition Data

• Released Date: 2015-05-20 
Deposition Author(s): Chen, X., Pu, H., Liu, L.

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

Revision History  

• 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