4QFU | pdb_00004qfu

Crystal structure of a glycoside hydrolase family 5 (BVU_2644) from Bacteroides vulgatus ATCC 8482 at 1.90 A resolution


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 
    0.172 (Depositor), 0.179 (DCC) 
  • R-Value Work: 
    0.142 (Depositor), 0.148 (DCC) 
  • R-Value Observed: 
    0.144 (Depositor) 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Crystal structure of a glycoside hydrolase family 5 (BVU_2644) from Bacteroides vulgatus ATCC 8482 at 1.90 A resolution

Joint Center for Structural Genomics (JCSG)

To be published.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
glycoside hydrolase family 5
A, B, C, D, E
484Phocaeicola vulgatus ATCC 8482Mutation(s): 0 
Gene Names: BVU_2644
UniProt
Find proteins for A6L3N2 (Phocaeicola vulgatus (strain ATCC 8482 / DSM 1447 / JCM 5826 / CCUG 4940 / NBRC 14291 / NCTC 11154))
Explore A6L3N2 
Go to UniProtKB:  A6L3N2
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA6L3N2
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
MRD
Query on MRD

Download Ideal Coordinates CCD File 
AA [auth E]
AB [auth L]
BA [auth E]
EA [auth F]
FA [auth F]
(4R)-2-METHYLPENTANE-2,4-DIOL
C6 H14 O2
SVTBMSDMJJWYQN-RXMQYKEDSA-N
SAR
Query on SAR

Download Ideal Coordinates CCD File 
KA [auth G],
U [auth C],
XA [auth K]
SARCOSINE
C3 H7 N O2
FSYKKLYZXJSNPZ-UHFFFAOYSA-N
NO3
Query on NO3

Download Ideal Coordinates CCD File 
CA [auth E],
GA [auth F],
R [auth B]
NITRATE ION
N O3
NHNBFGGVMKEFGY-UHFFFAOYSA-N
CL
Query on CL

Download Ideal Coordinates CCD File 
BB [auth L]
DA [auth E]
HA [auth F]
LA [auth G]
O [auth A]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
MSE
Query on MSE
A, B, C, D, E
L-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free:  0.172 (Depositor), 0.179 (DCC) 
  • R-Value Work:  0.142 (Depositor), 0.148 (DCC) 
  • R-Value Observed: 0.144 (Depositor) 
Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 115.95α = 91.6
b = 117.589β = 92.82
c = 125.249γ = 98.92
Software Package:
Software NamePurpose
MolProbitymodel building
PDB_EXTRACTdata extraction
SHELXphasing
SHARPphasing
XSCALEdata scaling
BUSTER-TNTrefinement
PHASERphasing
XDSdata reduction
SHELXDphasing
autoSHARPphasing
BUSTERrefinement

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2014-07-02
    Type: Initial release
  • Version 1.1: 2017-11-22
    Changes: Refinement description
  • Version 1.2: 2018-01-24
    Changes: Database references
  • Version 1.3: 2024-10-16
    Changes: Data collection, Database references, Derived calculations, Structure summary