4DNA | pdb_00004dna

CRYSTAL STRUCTURE OF putative glutathione reductase from Sinorhizobium meliloti 1021

• PDB DOI: https://doi.org/10.2210/pdb4DNA/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Sinorhizobium meliloti 1021
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2012-02-08 Released: 2012-03-21 
• Deposition Author(s): Malashkevich, V.N., Bhosle, R., Toro, R., Seidel, R., Almo, S.C., New York Structural Genomics Research Consortium (NYSGRC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.80 Å
• R-Value Free: 
  0.272 (Depositor), 0.270 (DCC) 
• R-Value Work: 
  0.208 (Depositor), 0.206 (DCC) 
• R-Value Observed: 
  0.211 (Depositor) 

Starting Model: experimental

Literature

CRYSTAL STRUCTURE OF putative glutathione reductase from Sinorhizobium meliloti 1021

Malashkevich, V.N., Bhosle, R., Toro, R., Seidel, R., Almo, S.C.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 102.67 kDa 
• Atom Count: 7,159 
• Modeled Residue Count: 922 
• Deposited Residue Count: 926 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Probable glutathione reductase	A, B	463	Sinorhizobium meliloti 1021	Mutation(s): 0  Gene Names: CAC46433.1, gor, R01854, SMc00154 EC: 1.8.1.7
UniProt
Find proteins for Q92PC0 (Rhizobium meliloti (strain 1021)) Explore Q92PC0  Go to UniProtKB:  Q92PC0

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
FAD	C [auth A], D [auth B]	FLAVIN-ADENINE DINUCLEOTIDE C27 H33 N9 O15 P2 VWWQXMAJTJZDQX-UYBVJOGSSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A, B	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.80 Å
• R-Value Free:  0.272 (Depositor), 0.270 (DCC) 
• R-Value Work:  0.208 (Depositor), 0.206 (DCC) 
• R-Value Observed: 0.211 (Depositor) 

Space Group: I 2 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 112.936	α = 90
b = 118.327	β = 90
c = 163.777	γ = 90

Software Package:

Software Name	Purpose
SCALEPACK	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
CBASS	data collection
HKL-2000	data reduction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2012-03-21 
Deposition Author(s): Malashkevich, V.N., Bhosle, R., Toro, R., Seidel, R., Almo, S.C., New York Structural Genomics Research Consortium (NYSGRC)

Revision History  

• Version 1.0: 2012-03-21
  Type: Initial release
  
• Version 1.1: 2023-09-13
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 1.2: 2023-12-06
  Changes: Data collection
• Version 1.3: 2024-11-20
  Changes: Structure summary