8ZJ5 | pdb_00008zj5

Terephthalate 1,2-cis-dihydrodioldehydrogenase/Decarboxylase in complex with 3,4-Dihydroxybenzoate.

• PDB DOI: https://doi.org/10.2210/pdb8ZJ5/pdb

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


• Deposited: 2024-05-14 Released: 2024-09-25 
• Deposition Author(s): Kumar, K.A., Pahwa, D., Kumar, P.
• Funding Organization(s): Department of Biotechnology (DBT, India)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.80 Å
• R-Value Free: 
  0.303 (Depositor), 0.306 (DCC) 
• R-Value Work: 
  0.260 (Depositor), 0.261 (DCC) 

Starting Model: in silico

Literature

Terephthalate 1,2-cis-dihydrodioldehydrogenase/Decarboxylase in complex with 3,4-Dihydroxybenzoate.

Kumar, K.A., Pahwa, D.

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: 141.49 kDa 
• Atom Count: 9,340 
• Modeled Residue Count: 1,249 
• Deposited Residue Count: 1,344 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
4-hydroxythreonine-4-phosphate dehydrogenase	A, B, C, D	336	Comamonas testosteroni KF-1	Mutation(s): 0  Gene Names: CtesDRAFT_PD2128 EC: 1.1.1.262
UniProt
Find proteins for B7WRJ7 (Comamonas testosteroni (strain DSM 14576 / KF-1)) Explore B7WRJ7  Go to UniProtKB:  B7WRJ7

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
DHB (Subject of Investigation/LOI)	F [auth C], H [auth D]	3,4-DIHYDROXYBENZOIC ACID C7 H6 O4 YQUVCSBJEUQKSH-UHFFFAOYSA-N
ZN (Subject of Investigation/LOI)	E [auth B], G [auth C], I [auth D], J [auth D]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.80 Å
• R-Value Free:  0.303 (Depositor), 0.306 (DCC) 
• R-Value Work:  0.260 (Depositor), 0.261 (DCC) 

Space Group: P 2 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 87.041	α = 90
b = 94.469	β = 90
c = 167.425	γ = 90

Software Package:

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

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2024-09-25 
Deposition Author(s): Kumar, K.A., Pahwa, D., Kumar, P.

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Funding Organization	Location	Grant Number
Department of Biotechnology (DBT, India)	India	DBT-2272-BIO-CNA

Revision History  

• Version 1.0: 2024-09-25
  Type: Initial release
  
• Version 1.1: 2024-10-09
  Changes: Derived calculations, Structure summary