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 1.5 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: 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 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)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
protein product of AT3G21360A, B330Arabidopsis thalianaMutation(s): 0 
Gene Names: At3g21360MHC9_4
EC: 1
UniProt
Find proteins for Q9LIG0 (Arabidopsis thaliana)
Explore Q9LIG0 
Go to UniProtKB:  Q9LIG0
Protein Feature View
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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

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Entry History 

Deposition Data

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