1Y0Z

X-ray structure of gene product from Arabidopsis thaliana At3g21360


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.241 
  • R-Value Work: 0.193 

wwPDB Validation   3D Report Full Report


This is version 1.6 of the entry. See complete history

Re-refinement Note

A newer entry is available that reflects an alternative modeling of the original data: 2Q4A


Literature

The structure at 2.4 A resolution of the protein from gene locus At3g21360, a putative Fe(II)/2-oxoglutarate-dependent enzyme from Arabidopsis thaliana.

Bitto, E.Bingman, C.A.Allard, S.T.Wesenberg, G.E.Aceti, D.J.Wrobel, R.L.Frederick, R.O.Sreenath, H.Vojtik, F.C.Jeon, W.B.Newman, C.S.Primm, J.Sussman, M.R.Fox, B.G.Markley, J.L.Phillips, G.N.

(2005) Acta Crystallogr Sect F Struct Biol Cryst Commun 61: 469-472

  • DOI: https://doi.org/10.1107/S1744309105011565
  • Primary Citation of Related Structures:  
    1Y0Z

  • PubMed Abstract: 

    The crystal structure of the gene product of At3g21360 from Arabidopsis thaliana was determined by the single-wavelength anomalous dispersion method and refined to an R factor of 19.3% (Rfree = 24.1%) at 2.4 A resolution. The crystal structure includes two monomers in the asymmetric unit that differ in the conformation of a flexible domain that spans residues 178-230. The crystal structure confirmed that At3g21360 encodes a protein belonging to the clavaminate synthase-like superfamily of iron(II) and 2-oxoglutarate-dependent enzymes. The metal-binding site was defined and is similar to the iron(II) binding sites found in other members of the superfamily.


  • Organizational Affiliation

    Center for Eukaryotic Structural Genomics, Department of Biochemistry, University of Wisconsin-Madison, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
protein product of AT3G21360
A, B
330Arabidopsis thalianaMutation(s): 0 
Gene Names: At3g21360
EC: 1
UniProt
Find proteins for Q9LIG0 (Arabidopsis thaliana)
Explore Q9LIG0 
Go to UniProtKB:  Q9LIG0
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9LIG0
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.241 
  • R-Value Work: 0.193 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 145.276α = 90
b = 61.094β = 121.68
c = 114.681γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing
RESOLVEphasing
CNSrefinement
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report



Entry History 

Revision History  (Full details and data files)

  • Version 1.0: 2004-11-30
    Type: Initial release
  • Version 1.1: 2008-04-30
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2011-07-27
    Changes: Version format compliance
  • Version 1.4: 2011-11-16
    Changes: Atomic model
  • Version 1.5: 2017-10-11
    Changes: Refinement description
  • Version 1.6: 2024-02-14
    Changes: Data collection, Database references, Derived calculations