6WGY | pdb_00006wgy

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

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 
    0.225 (Depositor), 0.230 (DCC) 
  • R-Value Work: 
    0.174 (Depositor), 0.180 (DCC) 
  • R-Value Observed: 
    0.175 (Depositor) 

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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.

Macromolecules
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(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Putative citrate synthase 2
A, B, C, D
380Mycobacterium tuberculosis variant bovis AF2122/97Mutation(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 Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP63778
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
CIT (Subject of Investigation/LOI)
Query on CIT
Download Ideal Coordinates CCD File 
HB [auth B],
KD [auth D]		CITRIC ACID
C6 H8 O7
KRKNYBCHXYNGOX-UHFFFAOYSA-N
IOD
Query on IOD
Download Ideal Coordinates CCD File 
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
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free:  0.225 (Depositor), 0.230 (DCC) 
  • R-Value Work:  0.174 (Depositor), 0.180 (DCC) 
  • R-Value Observed: 0.175 (Depositor) 
Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 127.14α = 90
b = 153.37β = 90
c = 100.58γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
XSCALEdata scaling
PHENIXrefinement
PDB_EXTRACTdata extraction
SHELXDEphasing
PHASERphasing
PARROTphasing
SHELXEmodel building
ARP/wARPmodel building
Cootmodel building

Structure Validation

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Ligand Structure Quality Assessment 


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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2020-04-22
    Type: Initial release
  • Version 1.1: 2024-03-06
    Changes: Data collection, Database references