4PPY | pdb_00004ppy

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)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 
  0.207 (Depositor), 0.210 (DCC) 
• R-Value Work: 
  0.185 (Depositor), 0.190 (DCC) 
• R-Value Observed: 
  0.186 (Depositor) 

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.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly 2  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content 

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

Macromolecules

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 / LMG 10263 / NCTC 9343 / Onslow / VPI 2553 / EN-2)) Explore Q5L8Y8  Go to UniProtKB:  Q5L8Y8

Small Molecules

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
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 (Depositor), 0.210 (DCC) 
• R-Value Work:  0.185 (Depositor), 0.190 (DCC) 
• R-Value Observed: 0.186 (Depositor) 

Diffraction Data: https://doi.org/10.18430/M34PPY

Space Group: C 1 2 1

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

Entry History 

Deposition Data

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

Revision History  

• 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
• Version 1.3: 2024-11-27
  Changes: Data collection, Structure summary