2OLC

Crystal structure of 5-methylthioribose kinase in complex with ADP-2Ho


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.250 
  • R-Value Work: 0.214 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

ADP-2Ho as a phasing tool for nucleotide-containing proteins.

Ku, S.Y.Smith, G.D.Howell, P.L.

(2007) Acta Crystallogr.,Sect.D 63: 493-499

  • DOI: 10.1107/S0907444907006592

  • PubMed Abstract: 
  • Trivalent holmium ions were shown to isomorphously replace magnesium ions to form an ADP-2Ho complex in the nucleotide-binding domain of Bacillus subtilis 5-methylthioribose (MTR) kinase. This nucleotide-holmium complex provided sufficient phasing po ...

    Trivalent holmium ions were shown to isomorphously replace magnesium ions to form an ADP-2Ho complex in the nucleotide-binding domain of Bacillus subtilis 5-methylthioribose (MTR) kinase. This nucleotide-holmium complex provided sufficient phasing power to allow SAD and SIRAS phasing of this previously unknown structure using the L(III) absorption edge of holmium. The structure of ADP-2Ho reveals that the two Ho ions are approximately 4 A apart and are likely to share their ligands: the phosphoryl O atoms of ADP and a water molecule. The structure determination of MTR kinase using data collected using Cu Kalpha X-radiation was also attempted. Although the heavy-atom substructure determination was successful, interpretation of the map was more challenging. The isomorphous substitution of holmium for magnesium in the MTR kinase-nucleotide complex suggests that this could be a useful phasing tool for other metal-dependent nucleotide-containing proteins.


    Organizational Affiliation

    Program in Molecular Structure and Function, Research Institute, Hospital for Sick Children, 555 University Avenue, Toronto, Ontario M5G 1X8, Canada.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Methylthioribose kinase
A, B
397Bacillus subtilis (strain 168)Mutation(s): 0 
Gene Names: mtnK (ykrT)
EC: 2.7.1.100
Find proteins for O31663 (Bacillus subtilis (strain 168))
Go to UniProtKB:  O31663
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ADP
Query on ADP

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Download CCD File 
A, B
ADENOSINE-5'-DIPHOSPHATE
C10 H15 N5 O10 P2
XTWYTFMLZFPYCI-KQYNXXCUSA-N
 Ligand Interaction
HO
Query on HO

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Download CCD File 
A, B
HOLMIUM ATOM
Ho
KJZYNXUDTRRSPN-UHFFFAOYSA-N
 Ligand Interaction
CPS
Query on CPS

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Download CCD File 
A
3-[(3-CHOLAMIDOPROPYL)DIMETHYLAMMONIO]-1-PROPANESULFONATE
CHAPS
C32 H58 N2 O7 S
UMCMPZBLKLEWAF-BCTGSCMUSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.250 
  • R-Value Work: 0.214 
  • Space Group: P 21 21 2
Unit Cell:
Length (Å)Angle (°)
a = 215.200α = 90.00
b = 83.600β = 90.00
c = 51.600γ = 90.00
Software Package:
Software NamePurpose
REFMACrefinement
RESOLVEphasing
PDB_EXTRACTdata extraction
SHELXphasing
d*TREKdata scaling
d*TREKdata reduction
CrystalCleardata collection
SHELXDEphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2007-05-22
    Type: Initial release
  • Version 1.1: 2008-05-01
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Advisory, Version format compliance