1Y0Z

X-ray structure of gene product from Arabidopsis thaliana At3g21360


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.4 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

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 61: 469-472

  • DOI: 10.1107/S1744309105011565

  • 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 includ ...

    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: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
protein product of AT3G21360
A, B
330Arabidopsis thalianaMutation(s): 0 
EC: 1.-.-.-
Find proteins for Q9LIG0 (Arabidopsis thaliana)
Go to UniProtKB:  Q9LIG0
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download SDF File 
Download CCD File 
A, B
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
FE2
Query on FE2

Download SDF File 
Download CCD File 
A, B
FE (II) ION
Fe
CWYNVVGOOAEACU-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.4 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 = 90.00
b = 61.094β = 121.68
c = 114.681γ = 90.00
Software Package:
Software NamePurpose
RESOLVEphasing
SCALEPACKdata scaling
CNSphasing
CNSrefinement
DENZOdata reduction
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2004-11-30
    Type: Initial release
  • Version 1.1: 2008-04-30
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance
  • Version 1.3: 2011-07-27
    Type: Version format compliance
  • Version 1.4: 2011-11-16
    Type: Atomic model
  • Version 1.5: 2017-10-11
    Type: Refinement description