4P93 | pdb_00004p93

Structure of Dienelactone Hydrolase at 1.85 A resolution crystallised in the C2 space group


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Free: 
    0.205 (Depositor), 0.210 (DCC) 
  • R-Value Work: 
    0.173 (Depositor), 0.175 (DCC) 
  • R-Value Observed: 
    0.175 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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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 F Struct Biol Commun 70: 884-889

  • DOI: https://doi.org/10.1107/S2053230X1401108X
  • Primary Citation Related Structures: 
    4P92, 4P93

  • 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 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.

Macromolecule Content 

  • Total Structure Weight: 50.99 kDa 
  • Atom Count: 3,738 
  • Modeled Residue Count: 466 
  • Deposited Residue Count: 472 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Carboxymethylenebutenolidase
A, B
236Pseudomonas knackmussiiMutation(s): 1 
Gene Names: clcD
EC: 3.1.1.45
UniProt
Find proteins for P0A115 (Pseudomonas knackmussii (strain DSM 6978 / CCUG 54928 / LMG 23759 / B13))
Explore P0A115 
Go to UniProtKB:  P0A115
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0A115
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Free:  0.205 (Depositor), 0.210 (DCC) 
  • R-Value Work:  0.173 (Depositor), 0.175 (DCC) 
  • R-Value Observed: 0.175 (Depositor) 
Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 100.23α = 90
b = 49.05β = 94.3
c = 89.61γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2014-07-09
    Type: Initial release
  • Version 1.1: 2014-10-15
    Changes: Database references
  • Version 1.2: 2023-12-20
    Changes: Data collection, Database references, Refinement description