8XVO | pdb_00008xvo

Crystal structure of a short-chain dehydrogenase/reductase 16 (SDR16) from Antrodia camphorata

PDB DOI: https://doi.org/10.2210/pdb8XVO/pdb

Classification: OXIDOREDUCTASE
Organism(s): Taiwanofungus camphoratus
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2024-01-15 Released: 2025-01-15
Deposition Author(s): Zhang, Y.Q., Zhang, M., Ye, M.
Funding Organization(s): National Natural Science Foundation of China (NSFC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.95 Å
R-Value Free:
0.203 (Depositor), 0.205 (DCC)
R-Value Work:
0.181 (Depositor), 0.182 (DCC)
R-Value Observed:
0.182 (Depositor)

Starting Model: in silico
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wwPDB Validation 3D Report Full Report

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

Literature

Crystal structure of a short-chain dehydrogenase/reductase 16 (SDR16) from Antrodia camphorata

Zhang, Y.Q., Zhang, M., Ye, M.

To be published.

Macromolecule Content

Total Structure Weight: 32.99 kDa
Atom Count: 2,372
Modeled Residue Count: 290
Deposited Residue Count: 303
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
short-chain dehydrogenase/reductase 16	A	303	Taiwanofungus camphoratus	Mutation(s): 0
UniProt
Find proteins for A0A165FX75 (Laetiporus sulphureus 93-53) Explore A0A165FX75 Go to UniProtKB: A0A165FX75
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0A165FX75
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
GOL Query on GOL 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]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.95 Å
R-Value Free: 0.203 (Depositor), 0.205 (DCC)
R-Value Work: 0.181 (Depositor), 0.182 (DCC)
R-Value Observed: 0.182 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 58.359	α = 90
b = 69.548	β = 90
c = 77.169	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
Aimless	data scaling

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2025-01-15

Deposition Author(s):

Funding Organization	Location	Grant Number
National Natural Science Foundation of China (NSFC)	China	--

Revision History (Full details and data files)

Version 1.0: 2025-01-15
Type: Initial release

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.