4MDC

Crystal structure of glutathione S-transferase from Sinorhizobium meliloti 1021, NYSGRC target 021389

• PDB DOI: https://doi.org/10.2210/pdb4MDC/pdb

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


• Deposited: 2013-08-22 Released: 2013-09-04 
• Deposition Author(s): Shabalin, I.G., Bacal, P., Cooper, D.R., Stead, M., Ahmed, M., Hammonds, J., Bonanno, J., Seidel, R., Almo, S.C., Minor, W., New York Structural Genomics Research Consortium (NYSGRC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.78 Å
• R-Value Free: 
  0.190 (Depositor), 0.190 (DCC) 
• R-Value Work: 
  0.161 (Depositor), 0.160 (DCC) 
• R-Value Observed: 
  0.163 (Depositor) 

Literature

Crystal structure of glutathione S-transferase from Sinorhizobium meliloti 1021

Shabalin, I.G., Bacal, P., Cooper, D.R., Stead, M., Ahmed, M., Hammonds, J., Bonanno, J., Seidel, R., Almo, S.C., Minor, W.

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)

Biological Assembly 2  

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

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 118.19 kDa 
• Atom Count: 8,596 
• Modelled Residue Count: 930 
• Deposited Residue Count: 1,008 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Putative glutathione S-transferase	A, B, C, D	252	Sinorhizobium meliloti 1021	Mutation(s): 0  Gene Names: gst4, R00327, SMc00407 EC: 2.5.1.18
UniProt
Find proteins for Q92SP3 (Rhizobium meliloti (strain 1021)) Explore Q92SP3  Go to UniProtKB:  Q92SP3

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GOL	E [auth A], F [auth A], G [auth B]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.78 Å
• R-Value Free:  0.190 (Depositor), 0.190 (DCC) 
• R-Value Work:  0.161 (Depositor), 0.160 (DCC) 
• R-Value Observed: 0.163 (Depositor) 

Diffraction Data: https://doi.org/10.18430/m30019

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 182.181	α = 90
b = 53.508	β = 115.88
c = 111.123	γ = 90

Software Package:

Software Name	Purpose
SCALEPACK	data scaling
SHELX	phasing
DM	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-3000	data collection
HKL-3000	data reduction
HKL-3000	data scaling
HKL-3000	phasing
SHELXD	phasing
MLPHARE	phasing
SOLVE	phasing
RESOLVE	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2013-09-04 
Deposition Author(s): Shabalin, I.G., Bacal, P., Cooper, D.R., Stead, M., Ahmed, M., Hammonds, J., Bonanno, J., Seidel, R., Almo, S.C., Minor, W., New York Structural Genomics Research Consortium (NYSGRC)

Revision History  

• Version 1.0: 2013-09-04
  Type: Initial release
  
• Version 1.1: 2022-04-13
  Changes: Database references, Derived calculations, Structure summary
• Version 1.2: 2024-11-20
  Changes: Data collection, Refinement description, Structure summary