1VQV | pdb_00001vqv

Crystal Structure of Thiamine Monophosphate Kinase (thil) from Aquifex Aeolicus

• PDB DOI: https://doi.org/10.2210/pdb1VQV/pdb
• Entry: 1VQV supersedes: 1YAW

• Classification: TRANSFERASE
• Organism(s): Aquifex aeolicus
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2005-01-05 Released: 2005-01-11 
• Deposition Author(s): Eswaramoorthy, S., Swaminathan, S., Burley, S.K., New York SGX Research Center for Structural Genomics (NYSGXRC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.65 Å
• R-Value Free: 
  0.260 (Depositor), 0.259 (DCC) 
• R-Value Work: 
  0.238 (Depositor), 0.237 (DCC) 
• R-Value Observed: 
  0.238 (Depositor) 

Literature

Crystal Structure of Thiamine Monophosphate Kinase (Thil) from Aquifex Aeolicus

Eswaramoorthy, S., Swaminathan, S.

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: 69.76 kDa 
• Atom Count: 4,732 
• Modeled Residue Count: 587 
• Deposited Residue Count: 612 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
thiamine monophosphate kinase	A, B	306	Aquifex aeolicus	Mutation(s): 5  EC: 2.7.4.16
UniProt
Find proteins for O67883 (Aquifex aeolicus (strain VF5)) Explore O67883  Go to UniProtKB:  O67883

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PO4	C [auth A], D [auth A], E [auth B], F [auth B]	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A, B	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.65 Å
• R-Value Free:  0.260 (Depositor), 0.259 (DCC) 
• R-Value Work:  0.238 (Depositor), 0.237 (DCC) 
• R-Value Observed: 0.238 (Depositor) 

Space Group: P 4₃

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 65.58	α = 90
b = 65.58	β = 90
c = 192.06	γ = 90

Software Package:

Software Name	Purpose
CBASS	data collection
HKL-2000	data reduction
SOLVE	phasing
CNS	refinement
HKL-2000	data scaling
SHARP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2005-01-11 
Deposition Author(s): Eswaramoorthy, S., Swaminathan, S., Burley, S.K., New York SGX Research Center for Structural Genomics (NYSGXRC)
• This entry supersedes: 1YAW

Revision History  

• Version 1.0: 2005-01-11
  Type: Initial release
  
• Version 1.1: 2008-04-27
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2021-02-03
  Changes: Database references, Derived calculations, Structure summary
• Version 1.4: 2023-12-27
  Changes: Advisory, Data collection, Database references
• Version 1.5: 2024-10-16
  Changes: Structure summary