4AM1

Crystal structure of the marine crustacean decapod shrimp (Litopenaeus vannamei) arginine kinase in the absence of substrate or ligands.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.25 Å
  • R-Value Free: 0.197 
  • R-Value Work: 0.158 
  • R-Value Observed: 0.161 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Crystallization and X-Ray Diffraction Studies of Arginine Kinase from the White Pacific Shrimp Litopenaeus Vannamei.

Lopez-Zavala, A.A.Sotelo-Mundo, R.R.Garcia-Orozco, K.D.Isac-Martinez, F.Brieba, L.G.Rudino-Pinera, E.

(2012) Acta Crystallogr Sect F Struct Biol Cryst Commun 68: 783

  • DOI: 10.1107/S1744309112020180
  • Primary Citation of Related Structures:  
    4AM1

  • PubMed Abstract: 
  • Crystals of an unligated monomeric arginine kinase from the Pacific whiteleg shrimp Litopenaeus vannamei (LvAK) were successfully obtained using the microbatch method. Crystallization conditions and preliminary X-ray diffraction analysis to 1.25 Å resolution are reported ...

    Crystals of an unligated monomeric arginine kinase from the Pacific whiteleg shrimp Litopenaeus vannamei (LvAK) were successfully obtained using the microbatch method. Crystallization conditions and preliminary X-ray diffraction analysis to 1.25 Å resolution are reported. Data were collected at 100 K on NSLS beamline X6A. The crystals belonged to space group P2(1)2(1)2(1), with unit-cell parameters a = 56.5, b = 70.2, c = 81.7 Å. One monomer per asymmetric unit was found, with a Matthews coefficient (V(M)) of 2.05 Å(3) Da(-1) and 40% solvent content. Initial phases were determined by molecular replacement using a homology model of LvAK as the search model. Refinement was performed with PHENIX, with final R(work) and R(free) values of 0.15 and 0.19, respectively. Biological analysis of the structure is currently in progress.


    Organizational Affiliation

    Laboratorio de Biología Molecular de Organismos Acuáticos, Centro de Investigación en Alimentación y Desarrollo A.C., Carretera a La Victoria km 0.6, Apartado Postal 1735, 83304 Hermosillo, SON, Mexico.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
ARGININE KINASEA356Penaeus vannameiMutation(s): 0 
EC: 2.7.3.3
UniProt
Find proteins for Q004B5 (Penaeus vannamei)
Explore Q004B5 
Go to UniProtKB:  Q004B5
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ004B5
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.25 Å
  • R-Value Free: 0.197 
  • R-Value Work: 0.158 
  • R-Value Observed: 0.161 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 56.72α = 90
b = 70.39β = 90
c = 81.99γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2012-07-11
    Type: Initial release
  • Version 1.1: 2012-07-18
    Changes: Structure summary