7Q9Z

Crystal structure of Chromobacterium violaceum aminotransferase in complex with PLP-pyruvate adduct

• PDB DOI: https://doi.org/10.2210/pdb7Q9Z/pdb

• Classification: TRANSFERASE
• Organism(s): Chromobacterium violaceum ATCC 12472
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2021-11-15 Released: 2022-11-23 
• Deposition Author(s): Isupov, M.N., Mitchell, D., Sayer, C., Littlechild, J.A.
• Funding Organization(s): Engineering and Physical Sciences Research Council, Biotechnology and Biological Sciences Research Council (BBSRC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.95 Å
• R-Value Free: 0.279 
• R-Value Work: 0.243 

Starting Model: experimental

Literature

Aminotransferase from Chromobacterium violaceum in complex with PLP-pyruvate adduct.

Isupov, M.N., Mitchell, D., Sayer, C., Littlechild, J.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.

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 110.69 kDa 
• Atom Count: 6,881 
• Modelled Residue Count: 854 
• Deposited Residue Count: 986 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Probable aminotransferase	A [auth AAA], B [auth BBB]	493	Chromobacterium violaceum ATCC 12472	Mutation(s): 0  Gene Names: CV_2025 EC: 2.6.1.62
UniProt
Find proteins for Q7NWG4 (Chromobacterium violaceum (strain ATCC 12472 / DSM 30191 / JCM 1249 / NBRC 12614 / NCIMB 9131 / NCTC 9757)) Explore Q7NWG4  Go to UniProtKB:  Q7NWG4

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
AN7 (Subject of Investigation/LOI)	C [auth AAA], H [auth BBB]	(3E)-4-{3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4-yl}-2-oxobut-3-enoic acid C11 H12 N O8 P FYMYHYJKCICXRI-NSCUHMNNSA-N
EDO	D [auth AAA], E [auth AAA], I [auth BBB], J [auth BBB], K [auth BBB]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N
CL	F [auth AAA]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M
NA	G [auth AAA], L [auth BBB]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.95 Å
• R-Value Free: 0.279 
• R-Value Work: 0.243 
• Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 58.15	α = 71.3
b = 60.72	β = 75.94
c = 61.8	γ = 85.73

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XSCALE	data scaling
MOLREP	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2022-11-23 
Deposition Author(s): Isupov, M.N., Mitchell, D., Sayer, C., Littlechild, J.A.

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Funding Organization	Location	Grant Number
Engineering and Physical Sciences Research Council	United Kingdom	EP/T002875/1
Biotechnology and Biological Sciences Research Council (BBSRC)	United Kingdom	BB/L002035/1

Revision History  

• Version 1.0: 2022-11-23
  Type: Initial release
  
• Version 1.1: 2024-01-31
  Changes: Data collection, Refinement description