4OVY

Crystal structure of Haloacid dehalogenase domain protein hydrolase from Planctomyces limnophilus DSM 3776


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Free: 0.175 
  • R-Value Work: 0.131 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Crystal structure of Haloacid dehalogenase domain protein hydrolase from Planctomyces limnophilus DSM 3776

Chang, C.Gu, M.Endres, M.Joachimiak, A.

To be published.

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Haloacid dehalogenase domain protein hydrolase
A
310Planctopirus limnophila (strain ATCC 43296 / DSM 3776 / IFAM 1008 / 290)Mutation(s): 0 
Find proteins for D5SUM3 (Planctopirus limnophila (strain ATCC 43296 / DSM 3776 / IFAM 1008 / 290))
Go to UniProtKB:  D5SUM3
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CIT
Query on CIT

Download SDF File 
Download CCD File 
A
CITRIC ACID
C6 H8 O7
KRKNYBCHXYNGOX-UHFFFAOYSA-N
 Ligand Interaction
CA
Query on CA

Download SDF File 
Download CCD File 
A
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
EDO
Query on EDO

Download SDF File 
Download CCD File 
A
1,2-ETHANEDIOL
ETHYLENE GLYCOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
MSE
Query on MSE
A
L-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Free: 0.175 
  • R-Value Work: 0.131 
  • Space Group: P 21 21 2
Unit Cell:
Length (Å)Angle (°)
a = 72.950α = 90.00
b = 75.502β = 90.00
c = 64.357γ = 90.00
Software Package:
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
SCALEPACKdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2014-02-05
    Type: Initial release
  • Version 1.1: 2015-02-25
    Type: Derived calculations
  • Version 1.2: 2017-11-22
    Type: Advisory, Database references, Derived calculations, Other, Refinement description, Source and taxonomy