3CTA

Crystal structure of riboflavin kinase from Thermoplasma acidophilum

• PDB DOI: https://doi.org/10.2210/pdb3CTA/pdb

• Classification: TRANSFERASE
• Organism(s): Thermoplasma acidophilum DSM 1728
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2008-04-11 Released: 2008-04-29 
• Deposition Author(s): Bonanno, J.B., Rutter, M., Bain, K.T., Mendoza, M., Romero, R., Smith, D., Wasserman, S., Sauder, J.M., Burley, S.K., Almo, S.C., New York SGX Research Center for Structural Genomics (NYSGXRC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 0.270 
• R-Value Work: 0.236 
• R-Value Observed: 0.237 

Literature

Crystal structure of riboflavin kinase from Thermoplasma acidophilum.

Bonanno, J.B., Rutter, M., Bain, K.T., Mendoza, M., Romero, R., Smith, D., Wasserman, S., Sauder, J.M., Burley, S.K., Almo, S.C.

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: 26.25 kDa 
• Atom Count: 1,476 
• Modelled Residue Count: 187 
• Deposited Residue Count: 230 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Riboflavin kinase	A	230	Thermoplasma acidophilum DSM 1728	Mutation(s): 0  Gene Names: rfk, Ta1064 EC: 2.7.1 (PDB Primary Data), 2.7.1.161 (UniProt)
UniProt
Find proteins for Q9HJA6 (Thermoplasma acidophilum (strain ATCC 25905 / DSM 1728 / JCM 9062 / NBRC 15155 / AMRC-C165)) Explore Q9HJA6  Go to UniProtKB:  Q9HJA6

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 0.270 
• R-Value Work: 0.236 
• R-Value Observed: 0.237 
• Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 77.087	α = 90
b = 82.987	β = 90
c = 80.544	γ = 90

Software Package:

Software Name	Purpose
SCALA	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
MAR345	data collection
MOSFLM	data reduction
SHELXCD	phasing
SHELXE	model building

Structure Validation

Entry History 

Deposition Data

• Released Date: 2008-04-29 
Deposition Author(s): Bonanno, J.B., Rutter, M., Bain, K.T., Mendoza, M., Romero, R., Smith, D., Wasserman, S., Sauder, J.M., Burley, S.K., Almo, S.C., New York SGX Research Center for Structural Genomics (NYSGXRC)

Revision History  

• Version 1.0: 2008-04-29
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2017-10-25
  Changes: Refinement description
• Version 1.3: 2018-11-14
  Changes: Data collection, Derived calculations, Structure summary
• Version 1.4: 2021-02-03
  Changes: Database references, Structure summary
• Version 1.5: 2024-02-21
  Changes: Data collection, Database references