3H7C

Crystal Structure of Arabidopsis thaliana Agmatine Deiminase from Cell Free Expression


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.50 Å
  • R-Value Free: 0.174 
  • R-Value Work: 0.146 
  • R-Value Observed: 0.147 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Structural Insights into the Catalytic Mechanism of Arabidopsis thaliana Agmatine Deiminase

Burgie, E.S.Bingman, C.A.Phillips Jr., G.N.

To be published.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Agmatine deiminaseA [auth X]383Arabidopsis thalianaMutation(s): 0 
Gene Names: AIHAt5g08170EMB1873T22D6.110
EC: 3.5.3.12
UniProt
Find proteins for Q8GWW7 (Arabidopsis thaliana)
Explore Q8GWW7 
Go to UniProtKB:  Q8GWW7
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8GWW7
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 6 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
1PE
Query on 1PE

Download Ideal Coordinates CCD File 
I [auth X]PENTAETHYLENE GLYCOL
C10 H22 O6
JLFNLZLINWHATN-UHFFFAOYSA-N
 Ligand Interaction
211
Query on 211

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H [auth X]2,2',2''-NITRILOTRIETHANOL
C6 H15 N O3
GSEJCLTVZPLZKY-UHFFFAOYSA-N
 Ligand Interaction
K
Query on K

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G [auth X]POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
 Ligand Interaction
CL
Query on CL

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B [auth X],
C [auth X]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
MG
Query on MG

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D [auth X]MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
NA
Query on NA

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E [auth X],
F [auth X]
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
MSE
Query on MSE
A [auth X]L-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.50 Å
  • R-Value Free: 0.174 
  • R-Value Work: 0.146 
  • R-Value Observed: 0.147 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 123.715α = 90
b = 69.932β = 98.4
c = 50.917γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
RESOLVEphasing
REFMACrefinement
PDB_EXTRACTdata extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
AutoSolphasing

Structure Validation

View Full Validation Report




Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2009-05-26
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2017-11-01
    Changes: Refinement description