4IS2

Crystal structure of the apo form of a 3alpha-hydroxysteroid dehydrogenase (BaiA2) associated with secondary bile acid synthesis from Clostridium scindens VPI12708 at 1.90 A resolution

PDB DOI: https://doi.org/10.2210/pdb4IS2/pdb

Classification: OXIDOREDUCTASE
Organism(s): [Clostridium] scindens
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2013-01-16 Released: 2013-04-03
Deposition Author(s): Joint Center for Structural Genomics (JCSG)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.90 Å
R-Value Free: 0.187
R-Value Work: 0.162
R-Value Observed: 0.163

wwPDB Validation 3D Report Full Report

This is version 1.4 of the entry. See complete history.

Literature

Crystal structure of the apo form of a 3alpha-hydroxysteroid dehydrogenase (BaiA2) associated with secondary bile acid synthesis from Clostridium scindens VPI12708 at 1.90 A resolution

Joint Center for Structural Genomics (JCSG)

To be published.

Macromolecule Content

Total Structure Weight: 29.38 kDa
Atom Count: 1,758
Modelled Residue Count: 215
Deposited Residue Count: 268
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Bile acid 3-alpha hydroxysteroid dehydrogenase	A	268	[Clostridium] scindens	Mutation(s): 0 Gene Names: baiA, BAIA2
UniProt
Find proteins for P19337 (Clostridium scindens (strain JCM 10418 / VPI 12708)) Explore P19337 Go to UniProtKB: P19337
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P19337
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A]	B [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE Query on MSE	A	L-PEPTIDE LINKING	C₅ H₁₁ N O₂ Se		MET

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.90 Å
R-Value Free: 0.187
R-Value Work: 0.162
R-Value Observed: 0.163
Space Group: I 2 2 2
Diffraction Data: https://doi.org/10.18430/M34IS2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 54.041	α = 90
b = 93.178	β = 90
c = 105.443	γ = 90

Software Package:

Software Name	Purpose
MolProbity	model building
PDB_EXTRACT	data extraction
SHELX	phasing
SHARP	phasing
SCALA	data scaling
REFMAC	refinement
MOSFLM	data reduction
SHELXD	phasing

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Released Date: 2013-04-03

Deposition Author(s):

Joint Center for Structural Genomics (JCSG)

Revision History (Full details and data files)

Version 1.0: 2013-04-03
Type: Initial release
Version 1.1: 2013-09-04
Changes: Structure summary
Version 1.2: 2017-11-15
Changes: Refinement description
Version 1.3: 2018-01-24
Changes: Database references
Version 1.4: 2023-02-01
Changes: Database references, Derived calculations

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), 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 R01GM133198.