1M15

Transition state structure of arginine kinase


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.20 Å
  • R-Value Free: 0.140 
  • R-Value Work: 0.125 
  • R-Value Observed: 0.127 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.5 of the entry. See complete history


Literature

Refinement of the arginine kinase transition-state analogue complex at 1.2 A resolution: mechanistic insights.

Yousef, M.S.Fabiola, F.Gattis, J.L.Somasundaram, T.Chapman, M.S.

(2002) Acta Crystallogr D Biol Crystallogr 58: 2009-2017

  • DOI: https://doi.org/10.1107/s0907444902014683
  • Primary Citation of Related Structures:  
    1M15

  • PubMed Abstract: 

    The three-dimensional crystal structure of an arginine kinase transition-state analogue complex has been refined at 1.2 A resolution, with an overall R factor of 12.3%. The current model provides a unique opportunity to analyze the structure of a bimolecular (phosphagen kinase) enzyme in its transition state. This atomic resolution structure confirms in-line transfer of the phosphoryl group and the catalytic importance of the precise alignment of the substrates. The structure is consistent with a concerted proton transfer that has been proposed for an unrelated kinase. Refinement of anisotropic temperature factors and translation-libration-screw (TLS) analyses led to the identification of four rigid groups and their prevalent modes of motion in the transition state. The relative magnitudes of the mobility of rigid groups are consistent with their proposed roles in catalysis.


  • Organizational Affiliation

    Institute of Molecular Biophysics, Florida State University, Tallahassee, FL 32306-4380, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
arginine kinase357Limulus polyphemusMutation(s): 0 
EC: 2.7.3.3
UniProt
Find proteins for P51541 (Limulus polyphemus)
Explore P51541 
Go to UniProtKB:  P51541
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP51541
Sequence Annotations
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  • Reference Sequence
Small Molecules
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.20 Å
  • R-Value Free: 0.140 
  • R-Value Work: 0.125 
  • R-Value Observed: 0.127 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 65.393α = 90
b = 70.312β = 90
c = 80.319γ = 90
Software Package:
Software NamePurpose
SHELXL-97refinement
SCALEPACKdata scaling
XDISPLAYF)data collection
CNSrefinement
SHELXmodel building
DENZOdata reduction
XDISPLAYF)data reduction
CNSphasing
SHELXphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2002-12-04
    Type: Initial release
  • Version 1.1: 2008-04-28
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2017-10-11
    Changes: Refinement description
  • Version 1.4: 2019-07-24
    Changes: Data collection, Refinement description
  • Version 1.5: 2024-02-14
    Changes: Data collection, Database references, Derived calculations, Refinement description