9W5P | pdb_00009w5p

Crystal structure of KRED

PDB DOI: https://doi.org/10.2210/pdb9W5P/pdb

Classification: OXIDOREDUCTASE
Organism(s): Novosphingobium aromaticivorans DSM 12444
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2025-08-01 Released: 2026-07-08
Deposition Author(s): Xu, H., Zhang, Z., Zhang, Y., Xu, Y., Zhang, L.
Funding Organization(s): Not funded

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.53 Å
R-Value Free:
0.275 (Depositor), 0.274 (DCC)
R-Value Work:
0.212 (Depositor), 0.216 (DCC)
R-Value Observed:
0.216 (Depositor)

Starting Model: in silico
View more details

wwPDB Validation 3D Report Full Report

Validation slider image for 9W5P

This is version 1.0 of the entry. See complete history.

Literature

Chemo-Enzymatic Synthesis of a Squalamine Intermediate by an Engineered Ketoreductase from Novosphingobium aromaticivorans

Zhang, Z., Zhang, Y., Du, Z., Zheng, X., Xu, H., Lin, Y., Kong, P., Li, H., Cao, J., Zhang, C., Li, S., Xu, Y., Zhang, L.

(2026) ACS Catal 16: 11618-11630

DOI: https://doi.org/10.1021/acscatal.6c03102

Macromolecule Content

Total Structure Weight: 107.32 kDa
Atom Count: 7,453
Modeled Residue Count: 1,030
Deposited Residue Count: 1,036
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Short-chain dehydrogenase/reductase SDR	A, B, C, D	259	Novosphingobium aromaticivorans DSM 12444	Mutation(s): 0 Gene Names: Saro_3543
UniProt
Find proteins for A4XEP2 (Novosphingobium aromaticivorans (strain ATCC 700278 / DSM 12444 / CCUG 56034 / CIP 105152 / NBRC 16084 / F199)) Explore A4XEP2 Go to UniProtKB: A4XEP2
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A4XEP2
Sequence Annotations Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.53 Å
R-Value Free: 0.275 (Depositor), 0.274 (DCC)
R-Value Work: 0.212 (Depositor), 0.216 (DCC)
R-Value Observed: 0.216 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 66.446	α = 90
b = 121.878	β = 90
c = 143.281	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
Aimless	data scaling
PDB_EXTRACT	data extraction
XDS	data reduction
REFMAC	phasing

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2026-07-08

Deposition Author(s):

Funding Organization	Location	Grant Number
Not funded		--

Revision History (Full details and data files)

Version 1.0: 2026-07-08
Type: Initial release

RCSB PDB is hosted by

RCSB PDB is a member of

RCSB Partners
Nucleic Acid Knowledgebase

CoreTrustSeal

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.