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), 0.268 (DCC)
R-Value Work:
0.175 (Depositor), 0.175 (DCC)
R-Value Observed:
0.184 (Depositor)

Starting Models: experimental
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Ligand Structure Quality Assessment

This is version 1.1 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

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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% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% 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), 0.268 (DCC)
R-Value Work: 0.175 (Depositor), 0.175 (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

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Ligand Structure Quality Assessment

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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
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.