5TRD

Structure of RbkR (Riboflavin Kinase) from Thermoplasma acidophilum determined in complex with CTP and its cognate DNA operator


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Free: 0.216 
  • R-Value Work: 0.174 
  • R-Value Observed: 0.176 

Starting Model: experimental
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This is version 1.1 of the entry. See complete history


Literature

Structure of RbkR (Riboflavin Kinase) from Thermoplasma acidophilum determined in complex with CTP and its cognate DNA operator

Vetting, M.W.Rodionova, I.A.Li, X.Osterman, A.L.Rodionov, D.A.Almo, S.C.

To be published.

Macromolecules

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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Riboflavin kinase
A, B
230Thermoplasma acidophilum DSM 1728Mutation(s): 0 
Gene Names: ribKTa1064
EC: 2.7.1.161
UniProt
Find proteins for Q9HJA6 (Thermoplasma acidophilum (strain ATCC 25905 / DSM 1728 / JCM 9062 / NBRC 15155 / AMRC-C165))
Explore Q9HJA6 
Go to UniProtKB:  Q9HJA6
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9HJA6
Sequence Annotations
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  • Reference Sequence

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Entity ID: 2
MoleculeChains LengthOrganismImage
DNA (5'-D(*AP*TP*TP*AP*CP*TP*AP*AP*TP*TP*CP*AP*CP*GP*AP*GP*TP*AP*A)-3')C [auth G]19Thermoplasma acidophilum
Sequence Annotations
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  • Reference Sequence

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Entity ID: 3
MoleculeChains LengthOrganismImage
DNA (5'-D(P*TP*TP*TP*AP*CP*TP*CP*GP*TP*GP*AP*AP*TP*TP*AP*GP*TP*AP*A)-3')D [auth H]19Thermoplasma acidophilum
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Free: 0.216 
  • R-Value Work: 0.174 
  • R-Value Observed: 0.176 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 58.411α = 90
b = 95.04β = 113.51
c = 61.262γ = 90
Software Package:
Software NamePurpose
Aimlessdata scaling
PHENIXrefinement
PDB_EXTRACTdata extraction

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2016-11-23
    Type: Initial release
  • Version 1.1: 2023-10-04
    Changes: Data collection, Database references, Derived calculations, Refinement description