6M2T | pdb_00006m2t

The crystal structure of benzoate coenzyme A ligase double mutant (H333A/I334A) in complex with 2-methyl-thiazole-5 carboxylate-AMP

• PDB DOI: https://doi.org/10.2210/pdb6M2T/pdb

• Classification: LIGASE
• Organism(s): Rhodopseudomonas palustris
• Expression System: Rhodopseudomonas palustris
• Mutation(s): Yes 


• Deposited: 2020-02-29 Released: 2021-03-03 
• Deposition Author(s): Li, T.L., Adhikari, K.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.14 Å
• R-Value Free: 
  0.198 (Depositor), 0.200 (DCC) 
• R-Value Work: 
  0.160 (Depositor), 0.170 (DCC) 
• R-Value Observed: 
  0.160 (Depositor) 

Starting Model: experimental

Literature

The crystal structure of benzoate coenzyme A ligase double mutant (H333A/I334A) in complex with 2-methyl-thiazole-5 carboxylate-AMP

Li, T.L., Adhikari, K., Malek, Z.S.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors.

Biological Assembly 3  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 3 assigned by authors.

Biological Assembly 4  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 4 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 228.69 kDa 
• Atom Count: 17,152 
• Modeled Residue Count: 2,072 
• Deposited Residue Count: 2,096 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Benzoate-coenzyme A ligase	A, B, C, D	524	Rhodopseudomonas palustris	Mutation(s): 4  Gene Names: badA
UniProt
Find proteins for Q93TK0 (Rhodopseudomonas palustris) Explore Q93TK0  Go to UniProtKB:  Q93TK0

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
AMP (Subject of Investigation/LOI)	E [auth A], G [auth B], I [auth C], K [auth D]	ADENOSINE MONOPHOSPHATE C10 H14 N5 O7 P UDMBCSSLTHHNCD-KQYNXXCUSA-N
6V9 (Subject of Investigation/LOI)	F [auth A], H [auth B], J [auth C], L [auth D]	2-methyl-1,3-thiazole-5-carboxylic acid C5 H5 N O2 S QCXCIYPOMMIBHO-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.14 Å
• R-Value Free:  0.198 (Depositor), 0.200 (DCC) 
• R-Value Work:  0.160 (Depositor), 0.170 (DCC) 
• R-Value Observed: 0.160 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 98.046	α = 90
b = 95.143	β = 110.58
c = 119.524	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHENIX	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2021-03-03 
Deposition Author(s): Li, T.L., Adhikari, K.

Revision History  

• Version 1.0: 2021-03-03
  Type: Initial release
  
• Version 2.0: 2023-11-15
  Changes: Atomic model, Data collection, Database references, Derived calculations
• Version 2.1: 2023-11-29
  Changes: Refinement description