3K94

Crystal Structure of Thiamin pyrophosphokinase from Geobacillus thermodenitrificans, Northeast Structural Genomics Consortium Target GtR2

• PDB DOI: https://doi.org/10.2210/pdb3K94/pdb

• Classification: TRANSFERASE
• Organism(s): Geobacillus thermodenitrificans NG80-2
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2009-10-15 Released: 2010-02-09 
• Deposition Author(s): Kuzin, A., Su, M., Seetharaman, J., Janjua, J., Xiao, R., Patel, D.J., Ciccosanti, C., Lee, D., Everett, J.K., Nair, R., Acton, T.B., Rost, B., Montelione, G.T., Hunt, J.F., Tong, L., Northeast Structural Genomics Consortium (NESG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 
  0.242 (Depositor), 0.230 (DCC) 
• R-Value Work: 
  0.177 (Depositor), 0.170 (DCC) 
• R-Value Observed: 
  0.180 (Depositor) 

Literature

Northeast Structural Genomics Consortium Target GtR2

Kuzin, A., Su, M., Seetharaman, J., Janjua, J., Xiao, R., Patel, D.J., Ciccosanti, C., Lee, D., Everett, J.K., Nair, R., Acton, T.B., Rost, B., Montelione, G.T., Hunt, J.F., Tong, L.

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: 50.97 kDa 
• Atom Count: 3,642 
• Modelled Residue Count: 431 
• Deposited Residue Count: 446 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Thiamin pyrophosphokinase	A, B	223	Geobacillus thermodenitrificans NG80-2	Mutation(s): 0  Gene Names: GTNG_1032 EC: 2.7.6.2
UniProt
Find proteins for A4IM54 (Geobacillus thermodenitrificans (strain NG80-2)) Explore A4IM54  Go to UniProtKB:  A4IM54

Small Molecules

Modified Residues  2 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
CSO	A, B	L-PEPTIDE LINKING	C3 H7 N O3 S		CYS
MSE	A, B	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free:  0.242 (Depositor), 0.230 (DCC) 
• R-Value Work:  0.177 (Depositor), 0.170 (DCC) 
• R-Value Observed: 0.180 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 68.422	α = 90
b = 73.652	β = 90
c = 82.657	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
PDB_EXTRACT	data extraction
ADSC	data collection
HKL-2000	data reduction
SCALEPACK	data scaling
PHENIX	phasing
REFMAC	refinement

Structure Validation

Entry History 

Deposition Data

• Released Date: 2010-02-09 
Deposition Author(s): Kuzin, A., Su, M., Seetharaman, J., Janjua, J., Xiao, R., Patel, D.J., Ciccosanti, C., Lee, D., Everett, J.K., Nair, R., Acton, T.B., Rost, B., Montelione, G.T., Hunt, J.F., Tong, L., Northeast Structural Genomics Consortium (NESG)

Revision History  

• Version 1.0: 2010-02-09
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Source and taxonomy, Version format compliance
• Version 1.2: 2019-07-17
  Changes: Data collection, Derived calculations, Refinement description
• Version 1.3: 2024-11-06
  Changes: Data collection, Database references, Structure summary