7E3X

Crystal structure of SDR family NAD(P)-dependent oxidoreductase from exiguobacterium

PDB DOI: https://doi.org/10.2210/pdb7E3X/pdb

Classification: OXIDOREDUCTASE
Organism(s): Exiguobacterium sp. KKBO11
Expression System: Escherichia coli BL21(DE3)
Mutation(s): Yes

Deposited: 2021-02-09 Released: 2021-09-29
Deposition Author(s): Chen, L., Tang, J., Yuan, S., Zhang, F., Chen, S.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.58 Å
R-Value Free: 0.255
R-Value Work: 0.192

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.1 of the entry. See complete history.

Literature

Structure-guided evolution of a ketoreductase forefficient and stereoselective bioreduction of bulkyalpha-aminobeta-keto esters

Tang, J., Chen, L., Zhang, L., Ni, G., Yu, J., Wang, H., Zhang, F., Yuan, S., Feng, M., Che, S.

(2021) Catal Sci Technol

DOI: https://doi.org/10.1039/d1cy01032h

Macromolecule Content

Total Structure Weight: 57.81 kDa
Atom Count: 3,974
Modelled Residue Count: 496
Deposited Residue Count: 510
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Oxidoreductase	A, B	255	Exiguobacterium sp. KKBO11	Mutation(s): 6 Gene Names: AYO36_14830
UniProt
Find proteins for A0A177S9P4 (Exiguobacterium sp. KKBO11) Explore A0A177S9P4 Go to UniProtKB: A0A177S9P4
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0A177S9P4
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NAP Query on NAP Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain D [auth B] MOL2 format, chain C [auth A] MOL2 format, chain D [auth B]	C [auth A], D [auth B]	NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE C₂₁ H₂₈ N₇ O₁₇ P₃ XJLXINKUBYWONI-NNYOXOHSSA-N		Interactions Focus chain C [auth A] Focus chain D [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.58 Å
R-Value Free: 0.255
R-Value Work: 0.192
Space Group: P 2₁ 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 68.464	α = 90
b = 71.167	β = 90
c = 115.158	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling
MOLREP	phasing

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2021-09-29

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2021-09-29
Type: Initial release
Version 1.1: 2023-11-29
Changes: Data collection, Refinement description

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM133198.