8HDE | pdb_00008hde

Brucella melitensis 7-alpha-Hydroxysteroid Dehydrogenase mutant: 1-53 truncation/I258M

PDB DOI: https://doi.org/10.2210/pdb8HDE/pdb

Classification: OXIDOREDUCTASE
Organism(s): Brucella melitensis
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2022-11-04 Released: 2024-01-03
Deposition Author(s): Liu, Z.Y., Zhang, R.Z.
Funding Organization(s): National Science Foundation (NSF, China)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.70 Å
R-Value Free:
0.267 (Depositor), 0.270 (DCC)
R-Value Work:
0.175 (Depositor), 0.180 (DCC)
R-Value Observed:
0.184 (Depositor)

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Structure of 7-alpha-hydroxysteroid dehydrogenase

Liu, Z.Y., Zhang, R.Z.

To be published.

Macromolecule Content

Total Structure Weight: 51.66 kDa
Atom Count: 3,646
Modeled Residue Count: 485
Deposited Residue Count: 502
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
7-alpha-hydroxysteroid dehydrogenase	A, B	251	Brucella melitensis	Mutation(s): 0 Gene Names: hdhA EC: 1.1.1.159
UniProt
Find proteins for Q8YIN7 (Brucella melitensis biotype 1 (strain ATCC 23456 / CCUG 17765 / NCTC 10094 / 16M)) Explore Q8YIN7 Go to UniProtKB: Q8YIN7
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q8YIN7
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
EDO (Subject of Investigation/LOI) Query on EDO Download Ideal Coordinates CCD File SDF format, chain D [auth B] SDF format, chain C [auth A] MOL2 format, chain D [auth B] MOL2 format, chain C [auth A] mmCIF format, chain D [auth B] mmCIF format, chain C [auth A]	C [auth A], D [auth B]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-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: 2.70 Å
R-Value Free: 0.267 (Depositor), 0.270 (DCC)
R-Value Work: 0.175 (Depositor), 0.180 (DCC)
R-Value Observed: 0.184 (Depositor)

Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 98.26	α = 90
b = 98.26	β = 90
c = 92.456	γ = 120

Software Package:

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

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2024-01-03

Deposition Author(s):

Funding Organization	Location	Grant Number
National Science Foundation (NSF, China)	China	31970045
National Science Foundation (NSF, China)	China	32271487

Revision History (Full details and data files)

Version 1.0: 2024-01-03
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.