4DA9

Crystal structure of putative Short-chain dehydrogenase/reductase from Sinorhizobium meliloti 1021

• PDB DOI: https://doi.org/10.2210/pdb4DA9/pdb

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


• Deposited: 2012-01-12 Released: 2012-01-25 
• 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: 2.50 Å
• R-Value Free: 0.231 
• R-Value Work: 0.177 
• R-Value Observed: 0.180 

Literature

Crystal structure of putative Short-chain dehydrogenase/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: Dihedral - D2  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

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 generated by PISA (software)

Biological Assembly 3  

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

Biological assembly 3 generated by PISA (software)

Biological Assembly 4  

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

Biological assembly 4 generated by PISA (software)

Biological Assembly 5  

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

Biological assembly 5 generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 118.94 kDa 
• Atom Count: 6,504 
• Modelled Residue Count: 874 
• Deposited Residue Count: 1,120 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Short-chain dehydrogenase/reductase	A, B, C, D	280	Sinorhizobium meliloti 1021	Mutation(s): 0  Gene Names: R03296, SMc04391 EC: 1.1.1.100
UniProt
Find proteins for Q92L02 (Rhizobium meliloti (strain 1021)) Explore Q92L02  Go to UniProtKB:  Q92L02

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	E [auth A], F [auth B], G [auth C], H [auth D]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

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: 2.50 Å
• R-Value Free: 0.231 
• R-Value Work: 0.177 
• R-Value Observed: 0.180 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 71.333	α = 90
b = 126.589	β = 90
c = 127.093	γ = 90

Software Package:

Software Name	Purpose
SCALEPACK	data scaling
SHELX	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
CBASS	data collection
HKL-3000	data reduction
SHELXD	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2012-01-25 
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: 2012-01-25
  Type: Initial release
  
• Version 1.1: 2014-04-02
  Changes: Other