2PHD | pdb_00002phd

Crystal Structure Determination of a Salicylate 1,2-Dioxygenase from Pseudaminobacter salicylatoxidans

• PDB DOI: https://doi.org/10.2210/pdb2PHD/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Pseudaminobacter salicylatoxidans
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2007-04-11 Released: 2008-04-22 
• Deposition Author(s): Matera, I., Ferraroni, M., Briganti, F.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.90 Å
• R-Value Free: 
  0.262 (Depositor), 0.260 (DCC) 
• R-Value Work: 
  0.193 (Depositor), 0.200 (DCC) 
• R-Value Observed: 
  0.197 (Depositor) 

Starting Model: experimental

Literature

Crystal Structure Determination of a Salicylate 1,2-Dioxygenase from Pseudaminobacter salicylatoxidans

Ferraroni, M., Matera, I., Briganti, F., Stolz, A., Burger, S.

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: 165.06 kDa 
• Atom Count: 11,032 
• Modeled Residue Count: 1,397 
• Deposited Residue Count: 1,472 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Gentisate 1,2-dioxygenase	A, B, C, D	368	Pseudaminobacter salicylatoxidans	Mutation(s): 1  EC: 1.13.11.4
UniProt
Find proteins for Q67FT0 (Pseudaminobacter salicylatoxidans) Explore Q67FT0  Go to UniProtKB:  Q67FT0

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ACT	G [auth A], N [auth D]	ACETATE ION C2 H3 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-M
FE	E [auth A], H [auth B], J [auth C], L [auth D]	FE (III) ION Fe VTLYFUHAOXGGBS-UHFFFAOYSA-N
CL	F [auth A], I [auth B], K [auth C], M [auth D]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.90 Å
• R-Value Free:  0.262 (Depositor), 0.260 (DCC) 
• R-Value Work:  0.193 (Depositor), 0.200 (DCC) 
• R-Value Observed: 0.197 (Depositor) 

Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 133.016	α = 90
b = 133.016	β = 90
c = 190.748	γ = 90

Software Package:

Software Name	Purpose
SCALA	data scaling
MOLREP	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
MAR345dtb	data collection
MOSFLM	data reduction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2008-04-22 
Deposition Author(s): Matera, I., Ferraroni, M., Briganti, F.

Revision History  

• Version 1.0: 2008-04-22
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2021-10-20
  Changes: Data collection, Database references, Derived calculations
• Version 1.3: 2023-08-30
  Changes: Data collection, Refinement description