4PPY

Crystal structure of a putative acylhydrolase (BF3764) from Bacteroides fragilis NCTC 9343 at 2.00 A resolution

PDB DOI: https://doi.org/10.2210/pdb4PPY/pdb

Classification: HYDROLASE
Organism(s): Bacteroides fragilis NCTC 9343
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2014-02-27 Released: 2014-04-02
Deposition Author(s): Joint Center for Structural Genomics (JCSG)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free: 0.207
R-Value Work: 0.185
R-Value Observed: 0.186

wwPDB Validation 3D Report Full Report

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

Literature

Crystal structure of a putative acylhydrolase (BF3764) from Bacteroides fragilis NCTC 9343 at 2.00 A resolution

Joint Center for Structural Genomics (JCSG)

To be published.

Macromolecule Content

Total Structure Weight: 70.53 kDa
Atom Count: 5,472
Modelled Residue Count: 625
Deposited Residue Count: 630
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Putative acylhydrolase	A, B, C	210	Bacteroides fragilis NCTC 9343	Mutation(s): 0 Gene Names: BF9343_3663
UniProt
Find proteins for Q5L8Y8 (Bacteroides fragilis (strain ATCC 25285 / DSM 2151 / CCUG 4856 / JCM 11019 / NCTC 9343 / Onslow)) Explore Q5L8Y8 Go to UniProtKB: Q5L8Y8
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q5L8Y8
Sequence Annotations Expand
Reference Sequence

Small Molecules

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

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free: 0.207
R-Value Work: 0.185
R-Value Observed: 0.186
Space Group: C 1 2 1
Diffraction Data: https://doi.org/10.18430/M34PPY

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 202.731	α = 90
b = 62.213	β = 95.9
c = 61.009	γ = 90

Software Package:

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

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Released Date: 2014-04-02

Deposition Author(s):

Joint Center for Structural Genomics (JCSG)

Revision History (Full details and data files)

Version 1.0: 2014-04-02
Type: Initial release
Version 1.1: 2017-11-22
Changes: Refinement description
Version 1.2: 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.