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)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.30 Å
R-Value Free:
0.140 (Depositor), 0.154 (DCC)
R-Value Work:
0.115 (Depositor)
R-Value Observed:
0.117 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.4 of the entry. See complete history.

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.

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

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| 3D Structure

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
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q92NR7
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NDP Query on NDP Download:Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE C₂₁ H₃₀ N₇ O₁₇ P₃ ACFIXJIJDZMPPO-NNYOXOHSSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.30 Å
R-Value Free: 0.140 (Depositor), 0.154 (DCC)
R-Value Work: 0.115 (Depositor)
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

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Ligand Structure Quality Assessment

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Entry History

& Funding Information

Deposition Data

Released Date: 2015-07-08

Deposition Author(s):

New York Structural Genomics Research Consortium (NYSGRC)

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

Revision History (Full details and data files)

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