Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 40.03 kDa 
• Atom Count: 3408 
• Modelled Residue Count: 345 
• Deposited Residue Count: 356 
• Unique protein chains: 1

4AM1

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

• PDB DOI: 10.2210/pdb4AM1/pdb

• Classification: TRANSFERASE
• Organism(s): Penaeus vannamei
• Mutation(s): No 


• Deposited: 2012-03-07 Released: 2012-07-11 
• Deposition Author(s): Lopez-Zavala, A.A., Sotelo-Mundo, R.R., Garcia-Orozco, K.D., Isac-Martinez, F., Brieba, L.G., Rudino-Pinera, E.

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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 

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

• PubMed: 22750864 
• 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. 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.

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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

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
ARGININE KINASE	A	356	Penaeus vannamei	Mutation(s): 0  EC: 2.7.3.3
UniProt
Find proteins for Q004B5 (Penaeus vannamei) Explore Q004B5  Go to UniProtKB:  Q004B5

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 = 56.72	α = 90
b = 70.39	β = 90
c = 81.99	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XSCALE	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2012-03-07 
• Released Date: 2012-07-11 
Deposition Author(s): Lopez-Zavala, A.A., Sotelo-Mundo, R.R., Garcia-Orozco, K.D., Isac-Martinez, F., Brieba, L.G., Rudino-Pinera, E.

Revision History  

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