2OMK | pdb_00002omk

Structure of the Bacteroides Thetaiotaomicron Thiamin Pyrophosphokinase

• PDB DOI: https://doi.org/10.2210/pdb2OMK/pdb

• Classification: TRANSFERASE
• Organism(s): Bacteroides thetaiotaomicron VPI-5482
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2007-01-22 Released: 2007-02-06 
• Deposition Author(s): Vorontsov, I.I., Minasov, G., Shuvalova, L., Abdullah, J., Collart, F.R., Joachimiak, A., Anderson, W.F., Midwest Center for Structural Genomics (MCSG)

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 
  0.200 (Depositor), 0.201 (DCC) 
• R-Value Work: 
  0.165 (Depositor), 0.164 (DCC) 
• R-Value Observed: 
  0.166 (Depositor) 

Literature

Structure of the Bacteroides Thetaiotaomicron Thiamin Pyrophosphokinase

Vorontsov, I.I., Minasov, G., Shuvalova, L., Abdullah, J., Collart, F.R., Joachimiak, A., Anderson, W.F.

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 and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 51.55 kDa 
• Atom Count: 4,145 
• Modeled Residue Count: 427 
• Deposited Residue Count: 462 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Hypothetical protein	A, B	231	Bacteroides thetaiotaomicron VPI-5482	Mutation(s): 2  Gene Names: BT_2397 EC: 2.7.6.2
UniProt
Find proteins for Q8A545 (Bacteroides thetaiotaomicron (strain ATCC 29148 / DSM 2079 / JCM 5827 / CCUG 10774 / NCTC 10582 / VPI-5482 / E50)) Explore Q8A545  Go to UniProtKB:  Q8A545

Small Molecules

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
SNN	A, B	L-PEPTIDE LINKING	C4 H6 N2 O2		ASN

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free:  0.200 (Depositor), 0.201 (DCC) 
• R-Value Work:  0.165 (Depositor), 0.164 (DCC) 
• R-Value Observed: 0.166 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 56.309	α = 90
b = 66.084	β = 99.9
c = 57.552	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
MAR345	data collection
HKL-2000	data reduction
HKL-2000	data scaling
PHENIX	phasing
SHELX	phasing
SHARP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2007-02-06 
Deposition Author(s): Vorontsov, I.I., Minasov, G., Shuvalova, L., Abdullah, J., Collart, F.R., Joachimiak, A., Anderson, W.F., Midwest Center for Structural Genomics (MCSG)

Revision History  

• Version 1.0: 2007-02-06
  Type: Initial release
  
• Version 1.1: 2008-05-01
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Source and taxonomy, Version format compliance
• Version 1.3: 2017-10-18
  Changes: Refinement description
• Version 1.4: 2021-10-20
  Changes: Database references, Derived calculations
• Version 2.0: 2023-11-15
  Changes: Atomic model, Data collection, Derived calculations
• Version 3.0: 2024-02-07
  Changes: Advisory, Atomic model, Data collection, Database references, Derived calculations, Non-polymer description, Polymer sequence, Source and taxonomy, Structure summary
• Version 3.1: 2024-10-30
  Changes: Structure summary