6WGY

Crystal structure of a Putative citrate synthase 2 from Mycobacterium bovis in complex with citrate

PDB DOI: https://doi.org/10.2210/pdb6WGY/pdb

Classification: TRANSFERASE
Organism(s): Mycobacterium tuberculosis variant bovis AF2122/97
Expression System: Escherichia coli 'BL21-Gold(DE3)pLysS AG
Mutation(s): No

Deposited: 2020-04-06 Released: 2020-04-22
Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.30 Å
R-Value Free: 0.225
R-Value Work: 0.174
R-Value Observed: 0.175

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Crystal structure of a Putative citrate synthase 2 from Mycobacterium bovis in complex with citrate

Abendroth, J., Yano, J.K., Horanyi, P.S., Lorimer, D.D., Edwards, T.E.

To be published.

Macromolecule Content

Total Structure Weight: 178.52 kDa
Atom Count: 12,071
Modelled Residue Count: 1,492
Deposited Residue Count: 1,520
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Putative citrate synthase 2	A, B, C, D	380	Mycobacterium tuberculosis variant bovis AF2122/97	Mutation(s): 0 Gene Names: citA, BQ2027_MB0913C EC: 2.3.3.16
UniProt
Find proteins for P63778 (Mycobacterium bovis (strain ATCC BAA-935 / AF2122/97)) Explore P63778 Go to UniProtKB: P63778
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P63778
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
CIT (Subject of Investigation/LOI) Query on CIT Download Ideal Coordinates CCD File SDF format, chain HB [auth B] SDF format, chain KD [auth D] MOL2 format, chain HB [auth B] MOL2 format, chain KD [auth D]	HB [auth B], KD [auth D]	CITRIC ACID C₆ H₈ O₇ KRKNYBCHXYNGOX-UHFFFAOYSA-N		Interactions Focus chain HB [auth B] Focus chain KD [auth D] Interactions & Density Focus chain HB [auth B] Focus chain KD [auth D]
IOD Query on IOD Download Ideal Coordinates CCD File SDF format, chain AA [auth A] SDF format, chain AB [auth B] SDF format, chain AC [auth C] SDF format, chain AD [auth D] SDF format, chain BA [auth A] SDF format, chain BB [auth B] SDF format, chain BC [auth C] SDF format, chain BD [auth D] SDF format, chain CA [auth A] SDF format, chain CB [auth B] SDF format, chain CC [auth C] SDF format, chain CD [auth D] SDF format, chain DA [auth A] SDF format, chain DB [auth B] SDF format, chain DC [auth C] SDF format, chain DD [auth D] SDF format, chain E [auth A] SDF format, chain EA [auth A] SDF format, chain EB [auth B] SDF format, chain EC [auth C] SDF format, chain ED [auth D] SDF format, chain F [auth A] SDF format, chain FA [auth A] SDF format, chain FB [auth B] SDF format, chain FC [auth C] SDF format, chain FD [auth D] SDF format, chain G [auth A] SDF format, chain GA [auth A] SDF format, chain GB [auth B] SDF format, chain GC [auth C] SDF format, chain GD [auth D] SDF format, chain H [auth A] SDF format, chain HA [auth A] SDF format, chain HC [auth C] SDF format, chain HD [auth D] SDF format, chain I [auth A] SDF format, chain IA [auth B] SDF format, chain IB [auth B] SDF format, chain IC [auth C] SDF format, chain ID [auth D] SDF format, chain J [auth A] SDF format, chain JA [auth B] SDF format, chain JB [auth C] SDF format, chain JC [auth C] SDF format, chain JD [auth D] SDF format, chain K [auth A] SDF format, chain KA [auth B] SDF format, chain KB [auth C] SDF format, chain KC [auth C] SDF format, chain L [auth A] SDF format, chain LA [auth B] SDF format, chain LB [auth C] SDF format, chain LC [auth D] SDF format, chain M [auth A] SDF format, chain MA [auth B] SDF format, chain MB [auth C] SDF format, chain MC [auth D] SDF format, chain N [auth A] SDF format, chain NA [auth B] SDF format, chain NB [auth C] SDF format, chain NC [auth D] SDF format, chain O [auth A] SDF format, chain OA [auth B] SDF format, chain OB [auth C] SDF format, chain OC [auth D] SDF format, chain P [auth A] SDF format, chain PA [auth B] SDF format, chain PB [auth C] SDF format, chain PC [auth D] SDF format, chain Q [auth A] SDF format, chain QA [auth B] SDF format, chain QB [auth C] SDF format, chain QC [auth D] SDF format, chain R [auth A] SDF format, chain RA [auth B] SDF format, chain RB [auth C] SDF format, chain RC [auth D] SDF format, chain S [auth A] SDF format, chain SA [auth B] SDF format, chain SB [auth C] SDF format, chain SC [auth D] SDF format, chain T [auth A] SDF format, chain TA [auth B] SDF format, chain TB [auth C] SDF format, chain TC [auth D] SDF format, chain U [auth A] SDF format, chain UA [auth B] SDF format, chain UB [auth C] SDF format, chain UC [auth D] SDF format, chain V [auth A] SDF format, chain VA [auth B] SDF format, chain VB [auth C] SDF format, chain VC [auth D] SDF format, chain W [auth A] SDF format, chain WA [auth B] SDF format, chain WB [auth C] SDF format, chain WC [auth D] SDF format, chain X [auth A] SDF format, chain XA [auth B] SDF format, chain XB [auth C] SDF format, chain XC [auth D] SDF format, chain Y [auth A] SDF format, chain YA [auth B] SDF format, chain YB [auth C] SDF format, chain YC [auth D] SDF format, chain Z [auth A] SDF format, chain ZA [auth B] SDF format, chain ZB [auth C] SDF format, chain ZC [auth D] MOL2 format, chain AA [auth A] MOL2 format, chain AB [auth B] MOL2 format, chain AC [auth C] MOL2 format, chain AD [auth D] MOL2 format, chain BA [auth A] MOL2 format, chain BB [auth B] MOL2 format, chain BC [auth C] MOL2 format, chain BD [auth D] MOL2 format, chain CA [auth A] MOL2 format, chain CB [auth B] MOL2 format, chain CC [auth C] MOL2 format, chain CD [auth D] MOL2 format, chain DA [auth A] MOL2 format, chain DB [auth B] MOL2 format, chain DC [auth C] MOL2 format, chain DD [auth D] MOL2 format, chain E [auth A] MOL2 format, chain EA [auth A] MOL2 format, chain EB [auth B] MOL2 format, chain EC [auth C] MOL2 format, chain ED [auth D] MOL2 format, chain F [auth A] MOL2 format, chain FA [auth A] MOL2 format, chain FB [auth B] MOL2 format, chain FC [auth C] MOL2 format, chain FD [auth D] MOL2 format, chain G [auth A] MOL2 format, chain GA [auth A] MOL2 format, chain GB [auth B] MOL2 format, chain GC [auth C] MOL2 format, chain GD [auth D] MOL2 format, chain H [auth A] MOL2 format, chain HA [auth A] MOL2 format, chain HC [auth C] MOL2 format, chain HD [auth D] MOL2 format, chain I [auth A] MOL2 format, chain IA [auth B] MOL2 format, chain IB [auth B] MOL2 format, chain IC [auth C] MOL2 format, chain ID [auth D] MOL2 format, chain J [auth A] MOL2 format, chain JA [auth B] MOL2 format, chain JB [auth C] MOL2 format, chain JC [auth C] MOL2 format, chain JD [auth D] MOL2 format, chain K [auth A] MOL2 format, chain KA [auth B] MOL2 format, chain KB [auth C] MOL2 format, chain KC [auth C] MOL2 format, chain L [auth A] MOL2 format, chain LA [auth B] MOL2 format, chain LB [auth C] MOL2 format, chain LC [auth D] MOL2 format, chain M [auth A] MOL2 format, chain MA [auth B] MOL2 format, chain MB [auth C] MOL2 format, chain MC [auth D] MOL2 format, chain N [auth A] MOL2 format, chain NA [auth B] MOL2 format, chain NB [auth C] MOL2 format, chain NC [auth D] MOL2 format, chain O [auth A] MOL2 format, chain OA [auth B] MOL2 format, chain OB [auth C] MOL2 format, chain OC [auth D] MOL2 format, chain P [auth A] MOL2 format, chain PA [auth B] MOL2 format, chain PB [auth C] MOL2 format, chain PC [auth D] MOL2 format, chain Q [auth A] MOL2 format, chain QA [auth B] MOL2 format, chain QB [auth C] MOL2 format, chain QC [auth D] MOL2 format, chain R [auth A] MOL2 format, chain RA [auth B] MOL2 format, chain RB [auth C] MOL2 format, chain RC [auth D] MOL2 format, chain S [auth A] MOL2 format, chain SA [auth B] MOL2 format, chain SB [auth C] MOL2 format, chain SC [auth D] MOL2 format, chain T [auth A] MOL2 format, chain TA [auth B] MOL2 format, chain TB [auth C] MOL2 format, chain TC [auth D] MOL2 format, chain U [auth A] MOL2 format, chain UA [auth B] MOL2 format, chain UB [auth C] MOL2 format, chain UC [auth D] MOL2 format, chain V [auth A] MOL2 format, chain VA [auth B] MOL2 format, chain VB [auth C] MOL2 format, chain VC [auth D] MOL2 format, chain W [auth A] MOL2 format, chain WA [auth B] MOL2 format, chain WB [auth C] MOL2 format, chain WC [auth D] MOL2 format, chain X [auth A] MOL2 format, chain XA [auth B] MOL2 format, chain XB [auth C] MOL2 format, chain XC [auth D] MOL2 format, chain Y [auth A] MOL2 format, chain YA [auth B] MOL2 format, chain YB [auth C] MOL2 format, chain YC [auth D] MOL2 format, chain Z [auth A] MOL2 format, chain ZA [auth B] MOL2 format, chain ZB [auth C] MOL2 format, chain ZC [auth D]	AA [auth A] AB [auth B] AC [auth C] AD [auth D] BA [auth A] AA [auth A], AB [auth B], AC [auth C], AD [auth D], BA [auth A], BB [auth B], BC [auth C], BD [auth D], CA [auth A], CB [auth B], CC [auth C], CD [auth D], DA [auth A], DB [auth B], DC [auth C], DD [auth D], E [auth A], EA [auth A], EB [auth B], EC [auth C], ED [auth D], F [auth A], FA [auth A], FB [auth B], FC [auth C], FD [auth D], G [auth A], GA [auth A], GB [auth B], GC [auth C], GD [auth D], H [auth A], HA [auth A], HC [auth C], HD [auth D], I [auth A], IA [auth B], IB [auth B], IC [auth C], ID [auth D], J [auth A], JA [auth B], JB [auth C], JC [auth C], JD [auth D], K [auth A], KA [auth B], KB [auth C], KC [auth C], L [auth A], LA [auth B], LB [auth C], LC [auth D], M [auth A], MA [auth B], MB [auth C], MC [auth D], N [auth A], NA [auth B], NB [auth C], NC [auth D], O [auth A], OA [auth B], OB [auth C], OC [auth D], P [auth A], PA [auth B], PB [auth C], PC [auth D], Q [auth A], QA [auth B], QB [auth C], QC [auth D], R [auth A], RA [auth B], RB [auth C], RC [auth D], S [auth A], SA [auth B], SB [auth C], SC [auth D], T [auth A], TA [auth B], TB [auth C], TC [auth D], U [auth A], UA [auth B], UB [auth C], UC [auth D], V [auth A], VA [auth B], VB [auth C], VC [auth D], W [auth A], WA [auth B], WB [auth C], WC [auth D], X [auth A], XA [auth B], XB [auth C], XC [auth D], Y [auth A], YA [auth B], YB [auth C], YC [auth D], Z [auth A], ZA [auth B], ZB [auth C], ZC [auth D]	IODIDE ION I XMBWDFGMSWQBCA-UHFFFAOYSA-M		Interactions Focus chain AA [auth A] Focus chain AB [auth B] Focus chain AC [auth C] Focus chain AD [auth D] Focus chain BA [auth A] Focus chain BB [auth B] Focus chain BC [auth C] Focus chain BD [auth D] Focus chain CA [auth A] Focus chain CB [auth B] Focus chain CC [auth C] Focus chain CD [auth D] Focus chain DA [auth A] Focus chain DB [auth B] Focus chain DC [auth C] Focus chain DD [auth D] Focus chain E [auth A] Focus chain EA [auth A] Focus chain EB [auth B] Focus chain EC [auth C] Focus chain ED [auth D] Focus chain F [auth A] Focus chain FA [auth A] Focus chain FB [auth B] Focus chain FC [auth C] Focus chain FD [auth D] Focus chain G [auth A] Focus chain GA [auth A] Focus chain GB [auth B] Focus chain GC [auth C] Focus chain GD [auth D] Focus chain H [auth A] Focus chain HA [auth A] Focus chain HC [auth C] Focus chain HD [auth D] Focus chain I [auth A] Focus chain IA [auth B] Focus chain IB [auth B] Focus chain IC [auth C] Focus chain ID [auth D] Focus chain J [auth A] Focus chain JA [auth B] Focus chain JB [auth C] Focus chain JC [auth C] Focus chain JD [auth D] Focus chain K [auth A] Focus chain KA [auth B] Focus chain KB [auth C] Focus chain KC [auth C] Focus chain L [auth A] Focus chain LA [auth B] Focus chain LB [auth C] Focus chain LC [auth D] Focus chain M [auth A] Focus chain MA [auth B] Focus chain MB [auth C] Focus chain MC [auth D] Focus chain N [auth A] Focus chain NA [auth B] Focus chain NB [auth C] Focus chain NC [auth D] Focus chain O [auth A] Focus chain OA [auth B] Focus chain OB [auth C] Focus chain OC [auth D] Focus chain P [auth A] Focus chain PA [auth B] Focus chain PB [auth C] Focus chain PC [auth D] Focus chain Q [auth A] Focus chain QA [auth B] Focus chain QB [auth C] Focus chain QC [auth D] Focus chain R [auth A] Focus chain RA [auth B] Focus chain RB [auth C] Focus chain RC [auth D] Focus chain S [auth A] Focus chain SA [auth B] Focus chain SB [auth C] Focus chain SC [auth D] Focus chain T [auth A] Focus chain TA [auth B] Focus chain TB [auth C] Focus chain TC [auth D] Focus chain U [auth A] Focus chain UA [auth B] Focus chain UB [auth C] Focus chain UC [auth D] Focus chain V [auth A] Focus chain VA [auth B] Focus chain VB [auth C] Focus chain VC [auth D] Focus chain W [auth A] Focus chain WA [auth B] Focus chain WB [auth C] Focus chain WC [auth D] Focus chain X [auth A] Focus chain XA [auth B] Focus chain XB [auth C] Focus chain XC [auth D] Focus chain Y [auth A] Focus chain YA [auth B] Focus chain YB [auth C] Focus chain YC [auth D] Focus chain Z [auth A] Focus chain ZA [auth B] Focus chain ZB [auth C] Focus chain ZC [auth D] Interactions & Density Focus chain AA [auth A] Focus chain AB [auth B] Focus chain AC [auth C] Focus chain AD [auth D] Focus chain BA [auth A] Focus chain BB [auth B] Focus chain BC [auth C] Focus chain BD [auth D] Focus chain CA [auth A] Focus chain CB [auth B] Focus chain CC [auth C] Focus chain CD [auth D] Focus chain DA [auth A] Focus chain DB [auth B] Focus chain DC [auth C] Focus chain DD [auth D] Focus chain E [auth A] Focus chain EA [auth A] Focus chain EB [auth B] Focus chain EC [auth C] Focus chain ED [auth D] Focus chain F [auth A] Focus chain FA [auth A] Focus chain FB [auth B] Focus chain FC [auth C] Focus chain FD [auth D] Focus chain G [auth A] Focus chain GA [auth A] Focus chain GB [auth B] Focus chain GC [auth C] Focus chain GD [auth D] Focus chain H [auth A] Focus chain HA [auth A] Focus chain HC [auth C] Focus chain HD [auth D] Focus chain I [auth A] Focus chain IA [auth B] Focus chain IB [auth B] Focus chain IC [auth C] Focus chain ID [auth D] Focus chain J [auth A] Focus chain JA [auth B] Focus chain JB [auth C] Focus chain JC [auth C] Focus chain JD [auth D] Focus chain K [auth A] Focus chain KA [auth B] Focus chain KB [auth C] Focus chain KC [auth C] Focus chain L [auth A] Focus chain LA [auth B] Focus chain LB [auth C] Focus chain LC [auth D] Focus chain M [auth A] Focus chain MA [auth B] Focus chain MB [auth C] Focus chain MC [auth D] Focus chain N [auth A] Focus chain NA [auth B] Focus chain NB [auth C] Focus chain NC [auth D] Focus chain O [auth A] Focus chain OA [auth B] Focus chain OB [auth C] Focus chain OC [auth D] Focus chain P [auth A] Focus chain PA [auth B] Focus chain PB [auth C] Focus chain PC [auth D] Focus chain Q [auth A] Focus chain QA [auth B] Focus chain QB [auth C] Focus chain QC [auth D] Focus chain R [auth A] Focus chain RA [auth B] Focus chain RB [auth C] Focus chain RC [auth D] Focus chain S [auth A] Focus chain SA [auth B] Focus chain SB [auth C] Focus chain SC [auth D] Focus chain T [auth A] Focus chain TA [auth B] Focus chain TB [auth C] Focus chain TC [auth D] Focus chain U [auth A] Focus chain UA [auth B] Focus chain UB [auth C] Focus chain UC [auth D] Focus chain V [auth A] Focus chain VA [auth B] Focus chain VB [auth C] Focus chain VC [auth D] Focus chain W [auth A] Focus chain WA [auth B] Focus chain WB [auth C] Focus chain WC [auth D] Focus chain X [auth A] Focus chain XA [auth B] Focus chain XB [auth C] Focus chain XC [auth D] Focus chain Y [auth A] Focus chain YA [auth B] Focus chain YB [auth C] Focus chain YC [auth D] Focus chain Z [auth A] Focus chain ZA [auth B] Focus chain ZB [auth C] Focus chain ZC [auth D]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.30 Å
R-Value Free: 0.225
R-Value Work: 0.174
R-Value Observed: 0.175
Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 127.14	α = 90
b = 153.37	β = 90
c = 100.58	γ = 90

Software Package:

Software Name	Purpose
XDS	data reduction
XSCALE	data scaling
PHENIX	refinement
PDB_EXTRACT	data extraction
SHELXDE	phasing
PHASER	phasing
PARROT	phasing
SHELXE	model building
ARP/wARP	model building
Coot	model building