3LAX | pdb_00003lax

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 (Depositor), 0.223 (DCC)
R-Value Work:
0.174 (Depositor), 0.172 (DCC)
R-Value Observed:
0.177 (Depositor)

wwPDB Validation 3D Report Full Report

Validation slider image for 3LAX

This is version 1.2 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
Modeled Residue Count: 106
Deposited Residue Count: 109
Unique protein chains: 1

Macromolecules

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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 EC: 6.2.1.30
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% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% 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 (Depositor), 0.223 (DCC)
R-Value Work: 0.174 (Depositor), 0.172 (DCC)
R-Value Observed: 0.177 (Depositor)

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

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View more in-depth experimental data

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
Version 1.2: 2024-11-06
Changes: Data collection, Database references, Derived calculations, 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.