3DDH

The structure of a putative haloacid dehalogenase-like family hydrolase from Bacteroides thetaiotaomicron VPI-5482


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.223 
  • R-Value Work: 0.177 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

The structure of a putative haloacid dehalogenase-like family hydrolase from Bacteroides thetaiotaomicron VPI-5482

Cuff, M.E.Duggan, E.Abdullah, J.Joachimiak, A.

To be published.

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Putative haloacid dehalogenase-like family hydrolase
A, B
234Bacteroides thetaiotaomicron (strain ATCC 29148 / DSM 2079 / NCTC 10582 / E50 / VPI-5482)Mutation(s): 0 
Find proteins for Q8A5Q8 (Bacteroides thetaiotaomicron (strain ATCC 29148 / DSM 2079 / NCTC 10582 / E50 / VPI-5482))
Go to UniProtKB:  Q8A5Q8
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CL
Query on CL

Download SDF File 
Download CCD File 
A, B
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 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
MG
Query on MG

Download SDF File 
Download CCD File 
A, B
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 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

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.223 
  • R-Value Work: 0.177 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 36.119α = 90.00
b = 104.222β = 90.00
c = 121.212γ = 90.00
Software Package:
Software NamePurpose
DMphasing
SCALEPACKdata scaling
DENZOdata reduction
SBC-Collectdata collection
Omodel building
RESOLVEphasing
MLPHAREphasing
PDB_EXTRACTdata extraction
Cootmodel building
SHELXDphasing
ARP/wARPmodel building
HKL-3000data reduction
HKL-3000phasing
REFMACrefinement
SOLVEphasing
CCP4phasing
HKL-3000data scaling
SHELXEmodel building

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2008-09-30
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Advisory, Version format compliance
  • Version 1.2: 2014-04-16
    Type: Experimental preparation
  • Version 1.3: 2017-10-25
    Type: Refinement description