3E38

CRYSTAL STRUCTURE OF A TWO-DOMAIN PROTEIN CONTAINING PREDICTED PHP-LIKE METAL-DEPENDENT PHOSPHOESTERASE (BVU_3505) FROM BACTEROIDES VULGATUS ATCC 8482 AT 2.20 A RESOLUTION


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Free: 0.225 
  • R-Value Work: 0.172 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Crystal structure of two-domain protein containing predicted PHP-like metal-dependent phosphoesterase (YP_001300751.1) from Bacteroides vulgatus ATCC 8482 at 2.20 A resolution

Joint Center for Structural Genomics (JCSG)

To be published.

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
two-domain protein containing predicted PHP-like metal-dependent phosphoesterase
A, B
343Bacteroides vulgatus (strain ATCC 8482 / DSM 1447 / JCM 5826 / NBRC 14291 / NCTC 11154)Mutation(s): 0 
Find proteins for A6L615 (Bacteroides vulgatus (strain ATCC 8482 / DSM 1447 / JCM 5826 / NBRC 14291 / NCTC 11154))
Go to UniProtKB:  A6L615
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download SDF File 
Download CCD File 
A, B
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
GOL
Query on GOL

Download SDF File 
Download CCD File 
A, B
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
CAC
Query on CAC

Download SDF File 
Download CCD File 
A, B
CACODYLATE ION
dimethylarsinate
C2 H6 As O2
OGGXGZAMXPVRFZ-UHFFFAOYSA-M
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
MSE
Query on MSE
A, B
L-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

Unit Cell:
Length (Å)Angle (°)
a = 95.680α = 90.00
b = 117.820β = 90.00
c = 79.560γ = 90.00
Software Package:
Software NamePurpose
REFMACrefinement
XSCALEdata scaling
MolProbitymodel building
PHENIXrefinement
XDSdata reduction
autoSHARPphasing
PDB_EXTRACTdata extraction
SHELXphasing
SHELXDphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2008-10-07
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Advisory, Version format compliance
  • Version 1.2: 2017-10-25
    Type: Refinement description
  • Version 1.3: 2019-07-24
    Type: Data collection, Derived calculations, Refinement description