9JDT | pdb_00009jdt

Crystal structure of reductase NaAD

PDB DOI: https://doi.org/10.2210/pdb9JDT/pdb

Classification: OXIDOREDUCTASE
Organism(s): Novosphingobium aromaticivorans DSM 12444
Expression System: Escherichia coli 'BL21-Gold(DE3)pLysS AG
Mutation(s): No

Deposited: 2024-09-01 Released: 2024-09-18
Deposition Author(s): Tang, J., Liuqing, C.
Funding Organization(s): Other private

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 3.26 Å
R-Value Free:
0.300 (Depositor), 0.317 (DCC)
R-Value Work:
0.260 (Depositor), 0.273 (DCC)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 9JDT

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

Literature

crystal structure of reductase LSADH

Tang, J., Liuqing, C.

To be published.

Macromolecule Content

Total Structure Weight: 444.86 kDa
Atom Count: 29,767
Modeled Residue Count: 4,090
Deposited Residue Count: 4,256
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, E A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P	266	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: 3.26 Å
R-Value Free: 0.300 (Depositor), 0.317 (DCC)
R-Value Work: 0.260 (Depositor), 0.273 (DCC)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 65.317	α = 90
b = 121.768	β = 93.4
c = 276.149	γ = 90

Software Package:

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

Structure Validation

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Entry History

& Funding Information

Deposition Data

Released Date: 2024-09-18

Deposition Author(s):

Funding Organization	Location	Grant Number
Other private		--

Revision History (Full details and data files)

Version 1.0: 2024-09-18
Type: Initial release
Version 1.1: 2026-03-11
Changes: Refinement description, Structure summary

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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.