2DVX

Crystal Structure of 2,6-Dihydroxybenzoate Decarboxylase Complexed with inhibitor 2,3-dihydroxybenzaldehyde


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free: 0.208 
  • R-Value Work: 0.184 
  • R-Value Observed: 0.184 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Crystal Structures of Nonoxidative Zn-Dependent 2,6-Dihydroxybenzoate (gamma-Resorcylate) Decarboxylase from Rhizobium sp. Strain MTP-10005

Goto, M.Hayashi, H.Miyahara, I.Hirotsu, K.Yoshida, M.Oikawa, T.

To be published.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Thermophilic reversible gamma-resorcylate decarboxylase
A, B, C, D
327Rhizobium sp. MTP-10005Mutation(s): 0 
EC: 4.1.1 (PDB Primary Data), 4.1.1.103 (UniProt)
UniProt
Find proteins for Q60GU1 (Rhizobium sp. (strain MTP-10005))
Explore Q60GU1 
Go to UniProtKB:  Q60GU1
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ60GU1
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
23A
Query on 23A

Download Ideal Coordinates CCD File 
F [auth A],
H [auth B],
J [auth C],
L [auth D]
2,3-DIHYDROXYBENZALDEHYDE
C7 H6 O3
IXWOUPGDGMCKGT-UHFFFAOYSA-N
ZN
Query on ZN

Download Ideal Coordinates CCD File 
E [auth A],
G [auth B],
I [auth C],
K [auth D]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free: 0.208 
  • R-Value Work: 0.184 
  • R-Value Observed: 0.184 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 109.02α = 90
b = 113.548β = 90
c = 119.322γ = 90
Software Package:
Software NamePurpose
CNSrefinement
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
AMoREphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

  • Released Date: 2006-09-19 
  • Deposition Author(s): Goto, M.

Revision History  (Full details and data files)

  • Version 1.0: 2006-09-19
    Type: Initial release
  • Version 1.1: 2008-04-30
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Source and taxonomy, Version format compliance
  • Version 1.3: 2023-10-25
    Changes: Data collection, Database references, Derived calculations, Refinement description