1UB0

Crystal Structure Analysis of Phosphomethylpyrimidine Kinase (ThiD) from Thermus Thermophilus Hb8

• PDB DOI: https://doi.org/10.2210/pdb1UB0/pdb

• Classification: TRANSFERASE
• Organism(s): Thermus thermophilus
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2003-03-26 Released: 2003-04-08 
• Deposition Author(s): Bagautdinov, B., Kuramitsu, S., Yokoyama, S., Miyano, M., Tahirov, T.H., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.05 Å
• R-Value Free: 0.232 
• R-Value Work: 0.207 

Literature

Crystal Structure Analysis of Phosphomethylpyrimidine Kinase (ThiD) from Thermus Thermophilus Hb8

Bagautdinov, B., Kuramitsu, S., Yokoyama, S., Miyano, M., Tahirov, T.H.

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,PQS (software)

Macromolecule Content

• Total Structure Weight: 27.46 kDa 
• Atom Count: 1,957 
• Modelled Residue Count: 246 
• Deposited Residue Count: 258 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Phosphomethylpyrimidine Kinase	A	258	Thermus thermophilus	Mutation(s): 0  Gene Names: ThiD EC: 2.7.4.7
UniProt
Find proteins for Q7SIA0 (Thermus thermophilus) Explore Q7SIA0  Go to UniProtKB:  Q7SIA0

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	B [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
GOL	E [auth A], F [auth A], G [auth A], H [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
DIO	C [auth A], D [auth A]	1,4-DIETHYLENE DIOXIDE C4 H8 O2 RYHBNJHYFVUHQT-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.05 Å
• R-Value Free: 0.232 
• R-Value Work: 0.207 
• Space Group: P 6₅ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 105.145	α = 90
b = 105.145	β = 90
c = 105.469	γ = 120

Software Package:

Software Name	Purpose
HKL-2000	data collection
SCALEPACK	data scaling
CNS	refinement
HKL-2000	data reduction
CNS	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2003-04-08 
Deposition Author(s): Bagautdinov, B., Kuramitsu, S., Yokoyama, S., Miyano, M., Tahirov, T.H., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

Revision History  

• Version 1.0: 2003-04-08
  Type: Initial release
  
• Version 1.1: 2008-04-27
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Derived calculations, Version format compliance
• Version 1.3: 2023-10-25
  Changes: Data collection, Database references, Derived calculations, Refinement description