4L8P

Crystal structure of a bile-acid 7-alpha dehydratase (CLOHIR_00079) from Clostridium hiranonis DSM 13275 at 1.60 A resolution

PDB DOI: https://doi.org/10.2210/pdb4L8P/pdb

Classification: LYASE
Organism(s): Peptacetobacter hiranonis DSM 13275
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2013-06-17 Released: 2013-08-21
Deposition Author(s): Joint Center for Structural Genomics (JCSG)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.60 Å
R-Value Free: 0.181
R-Value Work: 0.151
R-Value Observed: 0.153

wwPDB Validation 3D Report Full Report

This is version 1.3 of the entry. See complete history.

Literature

Crystal structure of a bile-acid 7-alpha dehydratase (CLOHIR_00079) from Clostridium hiranonis DSM 13275 at 1.60 A resolution

Joint Center for Structural Genomics (JCSG)

To be published.

Macromolecule Content

Total Structure Weight: 22.76 kDa
Atom Count: 1,559
Modelled Residue Count: 168
Deposited Residue Count: 187
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 7a-dehydratase, BaiE	A	187	Peptacetobacter hiranonis DSM 13275	Mutation(s): 0 Gene Names: baiE, CLOHIR_00079 EC: 4.2.1.106
UniProt
Find proteins for Q9RB47 (Peptacetobacter hiranonis (strain DSM 13275 / JCM 10541 / KCTC 15199 / TO-931)) Explore Q9RB47 Go to UniProtKB: Q9RB47
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q9RB47
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
1PE Query on 1PE Download Ideal Coordinates CCD File SDF format, chain E [auth A] MOL2 format, chain E [auth A] mmCIF format, chain E [auth A]	E [auth A]	PENTAETHYLENE GLYCOL C₁₀ H₂₂ O₆ JLFNLZLINWHATN-UHFFFAOYSA-N		Interactions Focus chain E [auth A]
PGE Query on PGE Download Ideal Coordinates CCD File SDF format, chain D [auth A] MOL2 format, chain D [auth A] mmCIF format, chain D [auth A]	D [auth A]	TRIETHYLENE GLYCOL C₆ H₁₄ O₄ ZIBGPFATKBEMQZ-UHFFFAOYSA-N		Interactions Focus chain D [auth A]
NI Query on NI 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]	NICKEL (II) ION Ni VEQPNABPJHWNSG-UHFFFAOYSA-N		Interactions Focus chain B [auth A]
NA Query on NA Download Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A] mmCIF format, chain C [auth A]	C [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain C [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: 1.60 Å
R-Value Free: 0.181
R-Value Work: 0.151
R-Value Observed: 0.153
Space Group: P 6₃
Diffraction Data: https://doi.org/10.18430/M34L8P

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 58.905	α = 90
b = 58.905	β = 90
c = 91.34	γ = 120

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: 2013-08-21

Deposition Author(s):

Joint Center for Structural Genomics (JCSG)

Revision History (Full details and data files)

Version 1.0: 2013-08-21
Type: Initial release
Version 1.1: 2017-11-15
Changes: Refinement description
Version 1.2: 2023-02-01
Changes: Database references, Derived calculations
Version 1.3: 2024-10-30
Changes: Data collection, Structure summary

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.