7Q9X | pdb_00007q9x

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

• PDB DOI: https://doi.org/10.2210/pdb7Q9X/pdb

• Classification: TRANSFERASE
• Organism(s): Chromobacterium violaceum ATCC 12472
• Expression System: Escherichia coli BL21
• 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: 1.60 Å
• R-Value Free: 
  0.261 (Depositor), 0.260 (DCC) 
• R-Value Work: 
  0.227 (Depositor), 0.230 (DCC) 

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

Biological Assembly 2  

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

Biological assembly 2 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 223.22 kDa 
• Atom Count: 17,188 
• Modeled Residue Count: 1,820 
• Deposited Residue Count: 1,972 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Probable aminotransferase	A [auth AAA], B [auth BBB], C [auth CCC], D [auth DDD]	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 / CCUG 213 / NBRC 12614 / NCIMB 9131 / NCTC 9757 / MK)) Explore Q7NWG4  Go to UniProtKB:  Q7NWG4

Small Molecules

Ligands 6 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
AN7 (Subject of Investigation/LOI)	E [auth AAA], SB [auth DDD], U [auth BBB], YA [auth CCC]	(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
PLP (Subject of Investigation/LOI)	W [auth BBB]	PYRIDOXAL-5'-PHOSPHATE C8 H10 N O6 P NGVDGCNFYWLIFO-UHFFFAOYSA-N
PEG	ZA [auth CCC]	DI(HYDROXYETHYL)ETHER C4 H10 O3 MTHSVFCYNBDYFN-UHFFFAOYSA-N
PO4	UB [auth DDD], X [auth BBB]	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K
EDO	AB [auth CCC], F [auth AAA], G [auth AAA], TB [auth DDD], V [auth BBB]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N
NA	AA [auth BBB], AC [auth DDD], BA [auth BBB], BB [auth CCC], BC [auth DDD], CA [auth BBB], CB [auth CCC], CC [auth DDD], DA [auth BBB], DB [auth CCC], DC [auth DDD], EA [auth BBB], EB [auth CCC], EC [auth DDD], FA [auth BBB], FB [auth CCC], FC [auth DDD], GA [auth BBB], GB [auth CCC], GC [auth DDD], H [auth AAA], HA [auth BBB], HB [auth CCC], HC [auth DDD], I [auth AAA], IA [auth BBB], IB [auth CCC], IC [auth DDD], J [auth AAA], JA [auth BBB], JB [auth CCC], JC [auth DDD], K [auth AAA], KA [auth BBB], KB [auth CCC], KC [auth DDD], L [auth AAA], LA [auth BBB], LB [auth CCC], LC [auth DDD], M [auth AAA], MA [auth BBB], MB [auth CCC], MC [auth DDD], N [auth AAA], NA [auth BBB], NB [auth CCC], NC [auth DDD], O [auth AAA], OA [auth BBB], OB [auth CCC], OC [auth DDD], P [auth AAA], PA [auth BBB], PB [auth CCC], PC [auth DDD], Q [auth AAA], QA [auth BBB], QB [auth CCC], R [auth AAA], RA [auth BBB], RB [auth CCC], S [auth AAA], SA [auth BBB], T [auth AAA], TA [auth BBB], UA [auth BBB], VA [auth BBB], VB [auth DDD], WA [auth BBB], WB [auth DDD], XA [auth BBB], XB [auth DDD], Y [auth BBB], YB [auth DDD], Z [auth BBB], ZB [auth DDD]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free:  0.261 (Depositor), 0.260 (DCC) 
• R-Value Work:  0.227 (Depositor), 0.230 (DCC) 

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 60.33	α = 103.56
b = 61.38	β = 89.38
c = 116.48	γ = 105.42

Software Package:

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