7Q9X

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)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.60 Å
R-Value Free: 0.261
R-Value Work: 0.227

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.1 of the entry. See complete history.

Literature

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

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

To be published.

Macromolecule Content

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

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

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 / NBRC 12614 / NCIMB 9131 / NCTC 9757)) Explore Q7NWG4 Go to UniProtKB: Q7NWG4
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q7NWG4
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 6 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
AN7 (Subject of Investigation/LOI) Query on AN7 Download Ideal Coordinates CCD File SDF format, chain E [auth AAA] SDF format, chain SB [auth DDD] SDF format, chain U [auth BBB] SDF format, chain YA [auth CCC] MOL2 format, chain E [auth AAA] MOL2 format, chain SB [auth DDD] MOL2 format, chain U [auth BBB] MOL2 format, chain YA [auth CCC]	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		Interactions Focus chain E [auth AAA] Focus chain SB [auth DDD] Focus chain U [auth BBB] Focus chain YA [auth CCC] Interactions & Density Focus chain E [auth AAA] Focus chain SB [auth DDD] Focus chain U [auth BBB] Focus chain YA [auth CCC]
PLP (Subject of Investigation/LOI) Query on PLP Download Ideal Coordinates CCD File SDF format, chain W [auth BBB] MOL2 format, chain W [auth BBB]	W [auth BBB]	PYRIDOXAL-5'-PHOSPHATE C₈ H₁₀ N O₆ P NGVDGCNFYWLIFO-UHFFFAOYSA-N		Interactions Focus chain W [auth BBB] Interactions & Density Focus chain W [auth BBB]
PEG Query on PEG Download Ideal Coordinates CCD File SDF format, chain ZA [auth CCC] MOL2 format, chain ZA [auth CCC]	ZA [auth CCC]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain ZA [auth CCC] Interactions & Density Focus chain ZA [auth CCC]
PO4 Query on PO4 Download Ideal Coordinates CCD File SDF format, chain UB [auth DDD] SDF format, chain X [auth BBB] MOL2 format, chain UB [auth DDD] MOL2 format, chain X [auth BBB]	UB [auth DDD], X [auth BBB]	PHOSPHATE ION O₄ P NBIIXXVUZAFLBC-UHFFFAOYSA-K		Interactions Focus chain UB [auth DDD] Focus chain X [auth BBB] Interactions & Density Focus chain UB [auth DDD] Focus chain X [auth BBB]
EDO Query on EDO Download Ideal Coordinates CCD File SDF format, chain AB [auth CCC] SDF format, chain F [auth AAA] SDF format, chain G [auth AAA] SDF format, chain TB [auth DDD] SDF format, chain V [auth BBB] MOL2 format, chain AB [auth CCC] MOL2 format, chain F [auth AAA] MOL2 format, chain G [auth AAA] MOL2 format, chain TB [auth DDD] MOL2 format, chain V [auth BBB]	AB [auth CCC], F [auth AAA], G [auth AAA], TB [auth DDD], V [auth BBB]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain AB [auth CCC] Focus chain F [auth AAA] Focus chain G [auth AAA] Focus chain TB [auth DDD] Focus chain V [auth BBB] Interactions & Density Focus chain AB [auth CCC] Focus chain F [auth AAA] Focus chain G [auth AAA] Focus chain TB [auth DDD] Focus chain V [auth BBB]
NA Query on NA Download Ideal Coordinates CCD File SDF format, chain AA [auth BBB] SDF format, chain AC [auth DDD] SDF format, chain BA [auth BBB] SDF format, chain BB [auth CCC] SDF format, chain BC [auth DDD] SDF format, chain CA [auth BBB] SDF format, chain CB [auth CCC] SDF format, chain CC [auth DDD] SDF format, chain DA [auth BBB] SDF format, chain DB [auth CCC] SDF format, chain DC [auth DDD] SDF format, chain EA [auth BBB] SDF format, chain EB [auth CCC] SDF format, chain EC [auth DDD] SDF format, chain FA [auth BBB] SDF format, chain FB [auth CCC] SDF format, chain FC [auth DDD] SDF format, chain GA [auth BBB] SDF format, chain GB [auth CCC] SDF format, chain GC [auth DDD] SDF format, chain H [auth AAA] SDF format, chain HA [auth BBB] SDF format, chain HB [auth CCC] SDF format, chain HC [auth DDD] SDF format, chain I [auth AAA] SDF format, chain IA [auth BBB] SDF format, chain IB [auth CCC] SDF format, chain IC [auth DDD] SDF format, chain J [auth AAA] SDF format, chain JA [auth BBB] SDF format, chain JB [auth CCC] SDF format, chain JC [auth DDD] SDF format, chain K [auth AAA] SDF format, chain KA [auth BBB] SDF format, chain KB [auth CCC] SDF format, chain KC [auth DDD] SDF format, chain L [auth AAA] SDF format, chain LA [auth BBB] SDF format, chain LB [auth CCC] SDF format, chain LC [auth DDD] SDF format, chain M [auth AAA] SDF format, chain MA [auth BBB] SDF format, chain MB [auth CCC] SDF format, chain MC [auth DDD] SDF format, chain N [auth AAA] SDF format, chain NA [auth BBB] SDF format, chain NB [auth CCC] SDF format, chain NC [auth DDD] SDF format, chain O [auth AAA] SDF format, chain OA [auth BBB] SDF format, chain OB [auth CCC] SDF format, chain OC [auth DDD] SDF format, chain P [auth AAA] SDF format, chain PA [auth BBB] SDF format, chain PB [auth CCC] SDF format, chain PC [auth DDD] SDF format, chain Q [auth AAA] SDF format, chain QA [auth BBB] SDF format, chain QB [auth CCC] SDF format, chain R [auth AAA] SDF format, chain RA [auth BBB] SDF format, chain RB [auth CCC] SDF format, chain S [auth AAA] SDF format, chain SA [auth BBB] SDF format, chain T [auth AAA] SDF format, chain TA [auth BBB] SDF format, chain UA [auth BBB] SDF format, chain VA [auth BBB] SDF format, chain VB [auth DDD] SDF format, chain WA [auth BBB] SDF format, chain WB [auth DDD] SDF format, chain XA [auth BBB] SDF format, chain XB [auth DDD] SDF format, chain Y [auth BBB] SDF format, chain YB [auth DDD] SDF format, chain Z [auth BBB] SDF format, chain ZB [auth DDD] MOL2 format, chain AA [auth BBB] MOL2 format, chain AC [auth DDD] MOL2 format, chain BA [auth BBB] MOL2 format, chain BB [auth CCC] MOL2 format, chain BC [auth DDD] MOL2 format, chain CA [auth BBB] MOL2 format, chain CB [auth CCC] MOL2 format, chain CC [auth DDD] MOL2 format, chain DA [auth BBB] MOL2 format, chain DB [auth CCC] MOL2 format, chain DC [auth DDD] MOL2 format, chain EA [auth BBB] MOL2 format, chain EB [auth CCC] MOL2 format, chain EC [auth DDD] MOL2 format, chain FA [auth BBB] MOL2 format, chain FB [auth CCC] MOL2 format, chain FC [auth DDD] MOL2 format, chain GA [auth BBB] MOL2 format, chain GB [auth CCC] MOL2 format, chain GC [auth DDD] MOL2 format, chain H [auth AAA] MOL2 format, chain HA [auth BBB] MOL2 format, chain HB [auth CCC] MOL2 format, chain HC [auth DDD] MOL2 format, chain I [auth AAA] MOL2 format, chain IA [auth BBB] MOL2 format, chain IB [auth CCC] MOL2 format, chain IC [auth DDD] MOL2 format, chain J [auth AAA] MOL2 format, chain JA [auth BBB] MOL2 format, chain JB [auth CCC] MOL2 format, chain JC [auth DDD] MOL2 format, chain K [auth AAA] MOL2 format, chain KA [auth BBB] MOL2 format, chain KB [auth CCC] MOL2 format, chain KC [auth DDD] MOL2 format, chain L [auth AAA] MOL2 format, chain LA [auth BBB] MOL2 format, chain LB [auth CCC] MOL2 format, chain LC [auth DDD] MOL2 format, chain M [auth AAA] MOL2 format, chain MA [auth BBB] MOL2 format, chain MB [auth CCC] MOL2 format, chain MC [auth DDD] MOL2 format, chain N [auth AAA] MOL2 format, chain NA [auth BBB] MOL2 format, chain NB [auth CCC] MOL2 format, chain NC [auth DDD] MOL2 format, chain O [auth AAA] MOL2 format, chain OA [auth BBB] MOL2 format, chain OB [auth CCC] MOL2 format, chain OC [auth DDD] MOL2 format, chain P [auth AAA] MOL2 format, chain PA [auth BBB] MOL2 format, chain PB [auth CCC] MOL2 format, chain PC [auth DDD] MOL2 format, chain Q [auth AAA] MOL2 format, chain QA [auth BBB] MOL2 format, chain QB [auth CCC] MOL2 format, chain R [auth AAA] MOL2 format, chain RA [auth BBB] MOL2 format, chain RB [auth CCC] MOL2 format, chain S [auth AAA] MOL2 format, chain SA [auth BBB] MOL2 format, chain T [auth AAA] MOL2 format, chain TA [auth BBB] MOL2 format, chain UA [auth BBB] MOL2 format, chain VA [auth BBB] MOL2 format, chain VB [auth DDD] MOL2 format, chain WA [auth BBB] MOL2 format, chain WB [auth DDD] MOL2 format, chain XA [auth BBB] MOL2 format, chain XB [auth DDD] MOL2 format, chain Y [auth BBB] MOL2 format, chain YB [auth DDD] MOL2 format, chain Z [auth BBB] MOL2 format, chain ZB [auth DDD]	AA [auth BBB] AC [auth DDD] BA [auth BBB] BB [auth CCC] BC [auth DDD] 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		Interactions Focus chain AA [auth BBB] Focus chain AC [auth DDD] Focus chain BA [auth BBB] Focus chain BB [auth CCC] Focus chain BC [auth DDD] Focus chain CA [auth BBB] Focus chain CB [auth CCC] Focus chain CC [auth DDD] Focus chain DA [auth BBB] Focus chain DB [auth CCC] Focus chain DC [auth DDD] Focus chain EA [auth BBB] Focus chain EB [auth CCC] Focus chain EC [auth DDD] Focus chain FA [auth BBB] Focus chain FB [auth CCC] Focus chain FC [auth DDD] Focus chain GA [auth BBB] Focus chain GB [auth CCC] Focus chain GC [auth DDD] Focus chain H [auth AAA] Focus chain HA [auth BBB] Focus chain HB [auth CCC] Focus chain HC [auth DDD] Focus chain I [auth AAA] Focus chain IA [auth BBB] Focus chain IB [auth CCC] Focus chain IC [auth DDD] Focus chain J [auth AAA] Focus chain JA [auth BBB] Focus chain JB [auth CCC] Focus chain JC [auth DDD] Focus chain K [auth AAA] Focus chain KA [auth BBB] Focus chain KB [auth CCC] Focus chain KC [auth DDD] Focus chain L [auth AAA] Focus chain LA [auth BBB] Focus chain LB [auth CCC] Focus chain LC [auth DDD] Focus chain M [auth AAA] Focus chain MA [auth BBB] Focus chain MB [auth CCC] Focus chain MC [auth DDD] Focus chain N [auth AAA] Focus chain NA [auth BBB] Focus chain NB [auth CCC] Focus chain NC [auth DDD] Focus chain O [auth AAA] Focus chain OA [auth BBB] Focus chain OB [auth CCC] Focus chain OC [auth DDD] Focus chain P [auth AAA] Focus chain PA [auth BBB] Focus chain PB [auth CCC] Focus chain PC [auth DDD] Focus chain Q [auth AAA] Focus chain QA [auth BBB] Focus chain QB [auth CCC] Focus chain R [auth AAA] Focus chain RA [auth BBB] Focus chain RB [auth CCC] Focus chain S [auth AAA] Focus chain SA [auth BBB] Focus chain T [auth AAA] Focus chain TA [auth BBB] Focus chain UA [auth BBB] Focus chain VA [auth BBB] Focus chain VB [auth DDD] Focus chain WA [auth BBB] Focus chain WB [auth DDD] Focus chain XA [auth BBB] Focus chain XB [auth DDD] Focus chain Y [auth BBB] Focus chain YB [auth DDD] Focus chain Z [auth BBB] Focus chain ZB [auth DDD] Interactions & Density Focus chain AA [auth BBB] Focus chain AC [auth DDD] Focus chain BA [auth BBB] Focus chain BB [auth CCC] Focus chain BC [auth DDD] Focus chain CA [auth BBB] Focus chain CB [auth CCC] Focus chain CC [auth DDD] Focus chain DA [auth BBB] Focus chain DB [auth CCC] Focus chain DC [auth DDD] Focus chain EA [auth BBB] Focus chain EB [auth CCC] Focus chain EC [auth DDD] Focus chain FA [auth BBB] Focus chain FB [auth CCC] Focus chain FC [auth DDD] Focus chain GA [auth BBB] Focus chain GB [auth CCC] Focus chain GC [auth DDD] Focus chain H [auth AAA] Focus chain HA [auth BBB] Focus chain HB [auth CCC] Focus chain HC [auth DDD] Focus chain I [auth AAA] Focus chain IA [auth BBB] Focus chain IB [auth CCC] Focus chain IC [auth DDD] Focus chain J [auth AAA] Focus chain JA [auth BBB] Focus chain JB [auth CCC] Focus chain JC [auth DDD] Focus chain K [auth AAA] Focus chain KA [auth BBB] Focus chain KB [auth CCC] Focus chain KC [auth DDD] Focus chain L [auth AAA] Focus chain LA [auth BBB] Focus chain LB [auth CCC] Focus chain LC [auth DDD] Focus chain M [auth AAA] Focus chain MA [auth BBB] Focus chain MB [auth CCC] Focus chain MC [auth DDD] Focus chain N [auth AAA] Focus chain NA [auth BBB] Focus chain NB [auth CCC] Focus chain NC [auth DDD] Focus chain O [auth AAA] Focus chain OA [auth BBB] Focus chain OB [auth CCC] Focus chain OC [auth DDD] Focus chain P [auth AAA] Focus chain PA [auth BBB] Focus chain PB [auth CCC] Focus chain PC [auth DDD] Focus chain Q [auth AAA] Focus chain QA [auth BBB] Focus chain QB [auth CCC] Focus chain R [auth AAA] Focus chain RA [auth BBB] Focus chain RB [auth CCC] Focus chain S [auth AAA] Focus chain SA [auth BBB] Focus chain T [auth AAA] Focus chain TA [auth BBB] Focus chain UA [auth BBB] Focus chain VA [auth BBB] Focus chain VB [auth DDD] Focus chain WA [auth BBB] Focus chain WB [auth DDD] Focus chain XA [auth BBB] Focus chain XB [auth DDD] Focus chain Y [auth BBB] Focus chain YB [auth DDD] Focus chain Z [auth BBB] Focus chain ZB [auth DDD]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.60 Å
R-Value Free: 0.261
R-Value Work: 0.227
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

View Full Validation Report

Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2022-11-23

Deposition Author(s):

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