5C7H | pdb_00005c7h

Crystal structure of aldo-keto reductase from Sinorhizobium meliloti 1021 in complex with NADPH

• PDB DOI: https://doi.org/10.2210/pdb5C7H/pdb

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


• Deposited: 2015-06-24 Released: 2015-07-08 
• Deposition Author(s): Gasiorowska, O.A., Shabalin, I.G., Handing, K.B., Seidel, R., Bonanno, J., Almo, S.C., Minor, W., New York Structural Genomics Research Consortium (NYSGRC)
• Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.30 Å
• R-Value Free: 
  0.140 (Depositor), 0.140 (DCC) 
• R-Value Work: 
  0.115 (Depositor), 0.120 (DCC) 
• R-Value Observed: 
  0.117 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of aldo-keto reductase from Sinorhizobium meliloti 1021 in complex with NADPH

Gasiorowska, O.A., Shabalin, I.G., Handing, K.B., Seidel, R., Bonanno, J., Almo, S.C., Minor, W., New York Structural Genomics Research Consortium (NYSGRC)

To be published.

Biological Assembly 1  

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

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

Macromolecule Content 

• Total Structure Weight: 31.5 kDa 
• Atom Count: 2,701 
• Modeled Residue Count: 281 
• Deposited Residue Count: 281 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Aldo-keto reductase	A	281	Sinorhizobium meliloti 1021	Mutation(s): 0  Gene Names: SMc01429 EC: 1.1.1
UniProt
Find proteins for Q92NR7 (Rhizobium meliloti (strain 1021)) Explore Q92NR7  Go to UniProtKB:  Q92NR7

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NDP	B [auth A]	NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE C21 H30 N7 O17 P3 ACFIXJIJDZMPPO-NNYOXOHSSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.30 Å
• R-Value Free:  0.140 (Depositor), 0.140 (DCC) 
• R-Value Work:  0.115 (Depositor), 0.120 (DCC) 
• R-Value Observed: 0.117 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 44.049	α = 90
b = 78.669	β = 90
c = 79.537	γ = 90

Software Package:

Software Name	Purpose
PDB_EXTRACT	data extraction
REFMAC	refinement
HKL-3000	phasing
MLPHARE	phasing
SHELX	phasing
HKL-3000	data scaling
HKL-3000	data reduction
BLU-MAX	data collection

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2015-07-08 
Deposition Author(s): Gasiorowska, O.A., Shabalin, I.G., Handing, K.B., Seidel, R., Bonanno, J., Almo, S.C., Minor, W., New York Structural Genomics Research Consortium (NYSGRC)

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	--

Revision History  

• Version 1.0: 2015-07-08
  Type: Initial release
  
• Version 1.1: 2017-11-22
  Changes: Derived calculations, Refinement description, Source and taxonomy, Structure summary
• Version 1.2: 2019-12-04
  Changes: Author supporting evidence
• Version 1.3: 2022-04-13
  Changes: Database references, Structure summary
• Version 1.4: 2023-09-27
  Changes: Data collection, Refinement description