1RKD

E. COLI RIBOKINASE COMPLEXED WITH RIBOSE AND ADP

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.84 Å
  • R-Value Free: 0.258 
  • R-Value Work: 0.220 
  • R-Value Observed: 0.221 

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Literature

Structure of Escherichia coli ribokinase in complex with ribose and dinucleotide determined to 1.8 A resolution: insights into a new family of kinase structures.

Sigrell, J.A., Cameron, A.D., Jones, T.A., Mowbray, S.L.

(1998) Structure 6: 183-193

  • DOI: https://doi.org/10.1016/s0969-2126(98)00020-3
  • Primary Citation of Related Structures:  
    1RKD

  • PubMed Abstract: 

    D-ribose must be phosphorylated at O5' before it can be used in either anabolism or catabolism. This reaction is catalysed by ribokinase and requires the presence of ATP and magnesium. Ribokinase is a member of a family of carbohydrate kinases of previously unknown structure.

    • Organizational Affiliation: 

    Department of Molecular Biology, Uppsala University, Sweden.


Macromolecules
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
RIBOKINASE309Escherichia coli K-12Mutation(s): 0 
Gene Names: RBSK
EC: 2.7.1.15
UniProt
Find proteins for P0A9J6 (Escherichia coli (strain K12))
Explore P0A9J6 
Go to UniProtKB:  P0A9J6
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0A9J6
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.84 Å
  • R-Value Free: 0.258 
  • R-Value Work: 0.220 
  • R-Value Observed: 0.221 
  • Space Group: P 61 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 95.4α = 90
b = 95.4β = 90
c = 154.87γ = 120
Software Package:
Software NamePurpose
MLPHAREphasing
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 1998-03-04
    Type: Initial release
  • Version 1.1: 2008-03-24
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Derived calculations, Source and taxonomy, Version format compliance
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Atomic model, Data collection, Derived calculations, Structure summary
  • Version 2.1: 2024-02-14
    Changes: Data collection, Database references, Structure summary