1M15

Transition state structure of arginine kinase


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.2 Å
  • R-Value Free: 0.140 
  • R-Value Work: 0.125 

wwPDB Validation 3D Report Full Report


This is version 1.3 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.,Sect.D 58: 2009-2017


  • 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 bim ...

    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.


    Related Citations: 
    • Critical Initial Real-Space Refinement in the Structure Determination of Arginine Kinase
      Zhou, G.,Somasundaram, T.,Blanc, E.,Chen, Z.,Chapman, M.S.
      (1999) Acta Crystallogr.,Sect.D 55: 835
    • Transition State Structure of Arginine Kinase: Implications for Catalysis of Bimolecular Reactions
      Zhou, G.,Somasundaram, T.,Blanc, E.,Parthasarathy, G.,Ellington, W.R.,Chapman, M.S.
      (1998) Proc.Natl.Acad.Sci.USA 95: 8449
    • Expression, Purification from Inclusion Bodies, and Crystal Characterization of a Transition State Analog Complex of Arginine Kinase: A Model for Studying Phosphagen Kinases
      Zhou, G.,Parthasarathy, G.,Somasundaram, T.,Ables, A.,Roy, L.,Strong, S.J.,Ellington, W.R.,Chapman, M.S.
      (1997) Protein Sci. 6: 444


    Organizational Affiliation

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




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
arginine kinase
A
357Limulus polyphemusEC: 2.7.3.3
Find proteins for P51541 (Limulus polyphemus)
Go to UniProtKB:  P51541
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ADP
Query on ADP

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

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Download CCD File 
A
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
ARG
Query on ARG

Download SDF File 
Download CCD File 
A
ARGININE
C6 H15 N4 O2
ODKSFYDXXFIFQN-BYPYZUCNSA-O
 Ligand Interaction
NO3
Query on NO3

Download SDF File 
Download CCD File 
A
NITRATE ION
N O3
NHNBFGGVMKEFGY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.2 Å
  • R-Value Free: 0.140 
  • R-Value Work: 0.125 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 65.393α = 90.00
b = 70.312β = 90.00
c = 80.319γ = 90.00
Software Package:
Software NamePurpose
SHELXL-97refinement
CNSphasing
SHELXmodel building
CNSrefinement
XDISPLAYF)data collection
XDISPLAYF)data reduction
DENZOdata reduction
SCALEPACKdata scaling
SHELXphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2002-12-04
    Type: Initial release
  • Version 1.1: 2008-04-28
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance
  • Version 1.3: 2017-10-11
    Type: Refinement description