4LGC | pdb_00004lgc

Crystal structure of a bile acid-coenzyme A ligase (baiB) from Clostridium scindens (VPI 12708) at 2.19 A resolution

PDB DOI: https://doi.org/10.2210/pdb4LGC/pdb

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

Deposited: 2013-06-27 Released: 2013-11-13
Deposition Author(s): Joint Center for Structural Genomics (JCSG)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.19 Å
R-Value Free:
0.228 (Depositor), 0.231 (DCC)
R-Value Work:
0.189 (Depositor), 0.194 (DCC)
R-Value Observed:
0.191 (Depositor)

wwPDB Validation 3D Report Full Report

This is version 1.2 of the entry. See complete history.

Literature

Crystal structure of a bile acid-coenzyme A ligase (baiB) from Clostridium scindens (VPI 12708) at 2.19 A resolution

Joint Center for Structural Genomics (JCSG)

To be published.

Macromolecule Content

Total Structure Weight: 61.57 kDa
Atom Count: 3,154
Modeled Residue Count: 393
Deposited Residue Count: 539
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-coenzyme A ligase	A	539	[Clostridium] scindens	Mutation(s): 0 Gene Names: BA20564A, baiB EC: 6 (PDB Primary Data), 6.2.1.7 (UniProt)
UniProt
Find proteins for P19409 (Clostridium scindens (strain JCM 10418 / VPI 12708)) Explore P19409 Go to UniProtKB: P19409
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P19409
Sequence Annotations Expand
Reference Sequence

Small Molecules

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: 2.19 Å
R-Value Free: 0.228 (Depositor), 0.231 (DCC)
R-Value Work: 0.189 (Depositor), 0.194 (DCC)
R-Value Observed: 0.191 (Depositor)

Diffraction Data: https://doi.org/10.18430/M34LGC

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 65.819	α = 90
b = 86.32	β = 90
c = 95.338	γ = 90

Software Package:

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

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Released Date: 2013-11-13

Deposition Author(s):

Joint Center for Structural Genomics (JCSG)

Revision History (Full details and data files)

Version 1.0: 2013-11-13
Type: Initial release
Version 1.1: 2017-11-15
Changes: Refinement description
Version 1.2: 2024-11-20
Changes: Data collection, Database references, Derived calculations, 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.