4P92

Crystal structure of dienelactone hydrolase C123S mutant at 1.65 A resolution


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.65 Å
  • R-Value Free: 0.172 
  • R-Value Work: 0.158 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Crystallization of dienelactone hydrolase in two space groups: structural changes caused by crystal packing.

Porter, J.L.Carr, P.D.Collyer, C.A.Ollis, D.L.

(2014) Acta Crystallogr.,Sect.F 70: 884-889

  • DOI: 10.1107/S2053230X1401108X
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Dienelactone hydrolase (DLH) is a monomeric protein with a simple α/β-hydrolase fold structure. It readily crystallizes in space group P2₁2₁2₁ from either a phosphate or ammonium sulfate precipitation buffer. Here, the structure of DLH at 1.85 Å reso ...

    Dienelactone hydrolase (DLH) is a monomeric protein with a simple α/β-hydrolase fold structure. It readily crystallizes in space group P2₁2₁2₁ from either a phosphate or ammonium sulfate precipitation buffer. Here, the structure of DLH at 1.85 Å resolution crystallized in space group C2 with two molecules in the asymmetric unit is reported. When crystallized in space group P2₁2₁2₁ DLH has either phosphates or sulfates bound to the protein in crucial locations, one of which is located in the active site, preventing substrate/inhibitor binding. Another is located on the surface of the enzyme coordinated by side chains from two different molecules. Crystallization in space group C2 from a sodium citrate buffer results in new crystallographic protein-protein interfaces. The protein backbone is highly similar, but new crystal contacts cause changes in side-chain orientations and in loop positioning. In regions not involved in crystal contacts, there is little change in backbone or side-chain configuration. The flexibility of surface loops and the adaptability of side chains are important factors enabling DLH to adapt and form different crystal lattices.


    Organizational Affiliation

    Research School of Chemistry, Australian National University, Building 137, Sullivans Creek Road, Canberra, ACT 0200, Australia.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Carboxymethylenebutenolidase
A
236Pseudomonas putidaMutation(s): 1 
Gene Names: clcD
EC: 3.1.1.45
Find proteins for P0A114 (Pseudomonas putida)
Go to UniProtKB:  P0A114
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download SDF File 
Download CCD File 
A
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.65 Å
  • R-Value Free: 0.172 
  • R-Value Work: 0.158 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 48.230α = 90.00
b = 70.980β = 90.00
c = 77.460γ = 90.00
Software Package:
Software NamePurpose
XDSdata reduction
REFMACrefinement
SCALEPACKdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2014-07-09
    Type: Initial release
  • Version 1.1: 2014-10-15
    Type: Database references
  • Version 1.2: 2014-12-10
    Type: Data collection