3LAX

The crystal structure of a domain of phenylacetate-coenzyme A ligase from Bacteroides vulgatus ATCC 8482

PDB DOI: https://doi.org/10.2210/pdb3LAX/pdb
Entry: 3LAX supersedes: 3GXS

Classification: LIGASE
Organism(s): Phocaeicola vulgatus ATCC 8482
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2010-01-07 Released: 2010-01-19
Deposition Author(s): Tan, K., Wu, R., Cobb, G., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.43 Å
R-Value Free: 0.225
R-Value Work: 0.174
R-Value Observed: 0.177

wwPDB Validation 3D Report Full Report

This is version 1.1 of the entry. See complete history.

Literature

The crystal structure of a domain of phenylacetate-coenzyme A ligase from Bacteroides vulgatus ATCC 8482

Tan, K., Wu, R., Cobb, G., Joachimiak, A.

To be published.

Macromolecule Content

Total Structure Weight: 12.47 kDa
Atom Count: 1,013
Modelled Residue Count: 106
Deposited Residue Count: 109
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Phenylacetate-coenzyme A ligase	A	109	Phocaeicola vulgatus ATCC 8482	Mutation(s): 0 Gene Names: Bacteroides vulgatus, BVU_1668
UniProt
Find proteins for A6L0Y5 (Phocaeicola vulgatus (strain ATCC 8482 / DSM 1447 / JCM 5826 / CCUG 4940 / NBRC 14291 / NCTC 11154)) Explore A6L0Y5 Go to UniProtKB: A6L0Y5
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A6L0Y5
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: 1.43 Å
R-Value Free: 0.225
R-Value Work: 0.174
R-Value Observed: 0.177
Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 33.737	α = 90
b = 44.334	β = 90
c = 67.601	γ = 90

Software Package:

Software Name	Purpose
SBC-Collect	data collection
SHELXD	phasing
MLPHARE	phasing
DM	model building
ARP	model building
WARP	model building
HKL-3000	phasing
PHENIX	refinement
HKL-3000	data reduction
HKL-3000	data scaling
DM	phasing

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Released Date: 2010-01-19

Deposition Author(s):

Midwest Center for Structural Genomics (MCSG)

This entry supersedes: 3GXS

Revision History (Full details and data files)

Version 1.0: 2010-01-19
Type: Initial release
Version 1.1: 2011-07-13
Changes: Version format compliance

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.