4AQK | pdb_00004aqk

Inositol 1,3,4,5,6-pentakisphosphate 2-kinase in complex with ADP and IP6


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 
    0.292 (Depositor), 0.287 (DCC) 
  • R-Value Work: 
    0.244 (Depositor), 0.241 (DCC) 
  • R-Value Observed: 
    0.246 (Depositor) 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 2.1 of the entry. See complete history

Literature

Expression, Purification, Crystallization and Preliminary X-Ray Diffraction Analysis of the Apo Form of Insp5 2-K from Arabidopsis Thaliana.

Banos-Sanz, J.I.Sanz-Aparicio, J.Brearley, C.A.Gonzalez, B.

(2012) Acta Crystallogr Sect F Struct Biol Cryst Commun 68: 701

  • DOI: https://doi.org/10.1107/S1744309112017307
  • Primary Citation Related Structures: 
    4AQK

  • PubMed Abstract: 

    Inositol 1,3,4,5,6-pentakisphosphate 2-kinase (IP(5) 2-K) is a key enzyme that catalyzes the synthesis of phytic acid (IP(6)) from inositol 1,3,4,5,6-pentakisphosphate (IP(5)) and ATP. The first structure of IP(5) 2-K, that from Arabidopsis thaliana, has been solved previously; it only crystallized in the presence of inositol, either the substrate IP(5) or the product IP(6), and failed to crystallize in its free state (without inositol). Based on structural analysis, a point mutation of IP(5) 2-K (W129A) has been produced in order to overcome this limitation and obtain information about protein conformational changes upon substrate binding. Here, the production and crystallization of W129A IP(5) 2-K in its free state and with bound nucleotide is described. These crystals differed from the native crystals and belonged to the orthorhombic space group P2(1)2(1)2, with unit-cell parameters a = 66.00, b = 68.23, c = 105.80 Å and a = 63.06, b = 71.80, c = 100.23 Å, respectively. The crystals diffracted to resolutions of 2.22 Å (apo) and 2.05 Å (nucleotide bound) using synchrotron radiation and contained one molecule per asymmetric unit. The structures have been determined using the molecular-replacement method and refinement is being undertaken.


  • Organizational Affiliation
    • Grupo de Cristalografía Macromolecular y Biología Estructural, Instituto de Química-Física Rocasolano, CSIC, Serrano 119, 28006 Madrid, Spain.

Macromolecule Content 

  • Total Structure Weight: 52.5 kDa 
  • Atom Count: 3,422 
  • Modeled Residue Count: 415 
  • Deposited Residue Count: 456 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
INOSITOL-PENTAKISPHOSPHATE 2-KINASE456Arabidopsis thalianaMutation(s): 0 
EC: 2.7.1.158
UniProt
Find proteins for Q93YN9 (Arabidopsis thaliana)
Explore Q93YN9 
Go to UniProtKB:  Q93YN9
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ93YN9
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free:  0.292 (Depositor), 0.287 (DCC) 
  • R-Value Work:  0.244 (Depositor), 0.241 (DCC) 
  • R-Value Observed: 0.246 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 62.11α = 90
b = 65.66β = 90
c = 121.79γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2012-05-02
    Type: Initial release
  • Version 1.1: 2014-02-05
    Changes: Database references
  • Version 2.0: 2020-10-07
    Changes: Atomic model, Data collection, Derived calculations, Non-polymer description, Other, Structure summary
  • Version 2.1: 2023-12-20
    Changes: Data collection, Database references, Refinement description