3BNW | pdb_00003bnw

Crystal structure of riboflavin kinase from Trypanosoma brucei

• PDB DOI: https://doi.org/10.2210/pdb3BNW/pdb

• Classification: TRANSFERASE
• Organism(s): Trypanosoma brucei
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2007-12-14 Released: 2008-01-08 
• Deposition Author(s): Merritt, E.A., Holmes, M., Structural Genomics of Pathogenic Protozoa Consortium (SGPP)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free: 
  0.289 (Depositor), 0.280 (DCC) 
• R-Value Work: 
  0.213 (Depositor), 0.220 (DCC) 
• R-Value Observed: 
  0.216 (Depositor) 

Starting Model: in silico

Literature

Riboflavin kinase from Trypanosoma brucei.

Merritt, E.A., Holmes, M.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PQS (software)

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors and generated by PQS (software)

Biological Assembly 3  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 3 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 41.25 kDa 
• Atom Count: 2,539 
• Modeled Residue Count: 317 
• Deposited Residue Count: 362 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Riboflavin kinase, putative	A, B	181	Trypanosoma brucei	Mutation(s): 0  Gene Names: Tb09.211.3420 EC: 2.7.1.26
UniProt
Find proteins for Q38DG4 (Trypanosoma brucei brucei (strain 927/4 GUTat10.1)) Explore Q38DG4  Go to UniProtKB:  Q38DG4

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free:  0.289 (Depositor), 0.280 (DCC) 
• R-Value Work:  0.213 (Depositor), 0.220 (DCC) 
• R-Value Observed: 0.216 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 39.695	α = 90
b = 65.604	β = 103.49
c = 62.69	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
Blu-Ice	data collection
MOSFLM	data reduction
SCALA	data scaling
SOLVE	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2008-01-08 
Deposition Author(s): Merritt, E.A., Holmes, M., Structural Genomics of Pathogenic Protozoa Consortium (SGPP)

Revision History  

• Version 1.0: 2008-01-08
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Advisory, Derived calculations, Version format compliance
• Version 1.2: 2024-02-21
  Changes: Data collection, Database references
• Version 1.3: 2024-04-03
  Changes: Refinement description