2DVX | pdb_00002dvx

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

• PDB DOI: https://doi.org/10.2210/pdb2DVX/pdb

• Classification: LYASE
• Organism(s): Rhizobium sp. MTP-10005
• Mutation(s): No 


• Deposited: 2006-08-01 Released: 2006-09-19 
• Deposition Author(s): Goto, M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free: 
  0.208 (Depositor), 0.207 (DCC) 
• R-Value Work: 
  0.184 (Depositor), 0.184 (DCC) 
• R-Value Observed: 
  0.184 (Depositor) 

Starting Model: experimental

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.

Biological Assembly 1  

Global Symmetry: Dihedral - D2  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 150.69 kDa 
• Atom Count: 11,585 
• Modeled Residue Count: 1,293 
• Deposited Residue Count: 1,308 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Thermophilic reversible gamma-resorcylate decarboxylase	A, B, C, D	327	Rhizobium sp. MTP-10005	Mutation(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

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
23A	F [auth A], H [auth B], J [auth C], L [auth D]	2,3-DIHYDROXYBENZALDEHYDE C7 H6 O3 IXWOUPGDGMCKGT-UHFFFAOYSA-N
ZN	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 (Depositor), 0.207 (DCC) 
• R-Value Work:  0.184 (Depositor), 0.184 (DCC) 
• R-Value Observed: 0.184 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 109.02	α = 90
b = 113.548	β = 90
c = 119.322	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
HKL-2000	data collection
HKL-2000	data reduction
HKL-2000	data scaling
AMoRE	phasing

Structure Validation

Entry History 

Deposition Data

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

Revision History  

• 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