7E24 | pdb_00007e24

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

PDB DOI: https://doi.org/10.2210/pdb7E24/pdb

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

Deposited: 2021-02-04 Released: 2021-09-29
Deposition Author(s): Chen, L., Tang, J., Yuan, S.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.72 Å
R-Value Free:
0.262 (Depositor), 0.270 (DCC)
R-Value Work:
0.208 (Depositor), 0.217 (DCC)

Starting Model: experimental
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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: 112.79 kDa
Atom Count: 7,908
Modeled Residue Count: 995
Deposited Residue Count: 1,004
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Oxidoreductase	A, B, C, D	251	Exiguobacterium acetylicum	Mutation(s): 9 Gene Names: ker
UniProt
Find proteins for Q6BDS0 (Exiguobacterium acetylicum) Explore Q6BDS0 Go to UniProtKB: Q6BDS0
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q6BDS0
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 E [auth A] SDF format, chain G [auth C] SDF format, chain H [auth D] SDF format, chain F [auth B] MOL2 format, chain E [auth A] MOL2 format, chain G [auth C] MOL2 format, chain H [auth D] MOL2 format, chain F [auth B] mmCIF format, chain E [auth A] mmCIF format, chain G [auth C] mmCIF format, chain H [auth D] mmCIF format, chain F [auth B]	E [auth A], F [auth B], G [auth C], H [auth D]	NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE C₂₁ H₂₈ N₇ O₁₇ P₃ XJLXINKUBYWONI-NNYOXOHSSA-N		Interactions Focus chain E [auth A] Focus chain F [auth B] Focus chain G [auth C] Focus chain H [auth D] Interactions & Density Focus chain E [auth A] Focus chain F [auth B] Focus chain G [auth C] Focus chain H [auth D]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.72 Å
R-Value Free: 0.262 (Depositor), 0.270 (DCC)
R-Value Work: 0.208 (Depositor), 0.217 (DCC)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 71.332	α = 90
b = 68.664	β = 90
c = 114.675	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
xia2	data reduction
Aimless	data scaling
MOLREP	phasing

Structure Validation

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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

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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 R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.