9JP7 | pdb_00009jp7

4,5-dihydroxyphthalate decarboxylase from Comamonas testosteroni (strain DSM 14576 / KF-1)

• PDB DOI: https://doi.org/10.2210/pdb9JP7/pdb

• Classification: LYASE
• Organism(s): Comamonas testosteroni KF-1
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2024-09-25 Released: 2024-10-30 
• Deposition Author(s): Kumar, K.A., Kumar, P.
• Funding Organization(s): Department of Biotechnology (DBT, India)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.05 Å
• R-Value Free: 
  0.335 (Depositor), 0.338 (DCC) 
• R-Value Work: 
  0.264 (Depositor), 0.265 (DCC) 

Starting Model: in silico

Literature

4,5-dihydroxyphthalate decarboxylase from Comamonas testosteroni (strain DSM 14576 / KF-1)

Kumar, K.A.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

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

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 157.83 kDa 
• Atom Count: 10,450 
• Modeled Residue Count: 1,289 
• Deposited Residue Count: 1,396 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
4,5-dihydroxyphthalate decarboxylase	A, B, C, D	349	Comamonas testosteroni KF-1	Mutation(s): 0  Gene Names: CtesDRAFT_PD2040 EC: 4.1.1.55
UniProt
Find proteins for B7WQU9 (Comamonas testosteroni (strain DSM 14576 / KF-1)) Explore B7WQU9  Go to UniProtKB:  B7WQU9

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ZN (Subject of Investigation/LOI)	E [auth A], F [auth B], G [auth C]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
MG (Subject of Investigation/LOI)	H [auth D]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.05 Å
• R-Value Free:  0.335 (Depositor), 0.338 (DCC) 
• R-Value Work:  0.264 (Depositor), 0.265 (DCC) 

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 128.045	α = 90
b = 270.201	β = 90
c = 113.627	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
CrysalisPro	data reduction
CrysalisPro	data scaling
MOLREP	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2024-10-30 
Deposition Author(s): Kumar, K.A., Kumar, P.

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Funding Organization	Location	Grant Number
Department of Biotechnology (DBT, India)	India	DBT-2771-BIO-CNA

Revision History  

• Version 1.0: 2024-10-30
  Type: Initial release