3UPT

Crystal structure of a transketolase from Burkholderia pseudomallei bound to TPP, calcium and ribose-5-phosphate


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.200 
  • R-Value Work: 0.151 
  • R-Value Observed: 0.153 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 2.1 of the entry. See complete history


Literature

Combining functional and structural genomics to sample the essential Burkholderia structome.

Baugh, L.Gallagher, L.A.Patrapuvich, R.Clifton, M.C.Gardberg, A.S.Edwards, T.E.Armour, B.Begley, D.W.Dieterich, S.H.Dranow, D.M.Abendroth, J.Fairman, J.W.Fox, D.Staker, B.L.Phan, I.Gillespie, A.Choi, R.Nakazawa-Hewitt, S.Nguyen, M.T.Napuli, A.Barrett, L.Buchko, G.W.Stacy, R.Myler, P.J.Stewart, L.J.Manoil, C.Van Voorhis, W.C.

(2013) PLoS One 8: e53851-e53851


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Transketolase
A, B
711Burkholderia thailandensis E264Mutation(s): 0 
Gene Names: BTH_I1195tkt
EC: 2.2.1.1
UniProt
Find proteins for Q2SZA7 (Burkholderia thailandensis (strain ATCC 700388 / DSM 13276 / CCUG 48851 / CIP 106301 / E264))
Explore Q2SZA7 
Go to UniProtKB:  Q2SZA7
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ2SZA7
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
TPP
Query on TPP

Download Ideal Coordinates CCD File 
D [auth A],
J [auth B]
THIAMINE DIPHOSPHATE
C12 H19 N4 O7 P2 S
AYEKOFBPNLCAJY-UHFFFAOYSA-O
RP5
Query on RP5

Download Ideal Coordinates CCD File 
E [auth A],
F [auth A]
5-O-phosphono-beta-D-ribofuranose
C5 H11 O8 P
KTVPXOYAKDPRHY-TXICZTDVSA-N
BR
Query on BR

Download Ideal Coordinates CCD File 
G [auth A],
H [auth A],
K [auth B],
L [auth B]
BROMIDE ION
Br
CPELXLSAUQHCOX-UHFFFAOYSA-M
CA
Query on CA

Download Ideal Coordinates CCD File 
C [auth A],
I [auth B]
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.200 
  • R-Value Work: 0.151 
  • R-Value Observed: 0.153 
  • Space Group: P 41 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 146.98α = 90
b = 146.98β = 90
c = 142.87γ = 90
Software Package:
Software NamePurpose
XSCALEdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
XDSdata reduction

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2011-12-14
    Type: Initial release
  • Version 1.1: 2013-10-30
    Changes: Database references
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Atomic model, Data collection, Database references, Derived calculations
  • Version 2.1: 2023-09-13
    Changes: Data collection, Database references, Refinement description, Structure summary