3H7C

Crystal Structure of Arabidopsis thaliana Agmatine Deiminase from Cell Free Expression


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.5 Å
  • R-Value Free: 0.174 
  • R-Value Work: 0.146 

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: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Agmatine deiminase
X
383Arabidopsis thalianaGene Names: AIH (EMB1873)
EC: 3.5.3.12
Find proteins for Q8GWW7 (Arabidopsis thaliana)
Go to UniProtKB:  Q8GWW7
Small Molecules
Ligands 6 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
K
Query on K

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X
POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
 Ligand Interaction
NA
Query on NA

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X
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
CL
Query on CL

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X
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
MG
Query on MG

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X
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
211
Query on 211

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X
2,2',2''-NITRILOTRIETHANOL
C6 H15 N O3
GSEJCLTVZPLZKY-UHFFFAOYSA-N
 Ligand Interaction
1PE
Query on 1PE

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X
PENTAETHYLENE GLYCOL
PEG400
C10 H22 O6
JLFNLZLINWHATN-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
MSE
Query on MSE
X
L-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.5 Å
  • R-Value Free: 0.174 
  • R-Value Work: 0.146 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 123.715α = 90.00
b = 69.932β = 98.40
c = 50.917γ = 90.00
Software Package:
Software NamePurpose
AutoSolphasing
DENZOdata reduction
PDB_EXTRACTdata extraction
HKL-2000data collection
REFMACrefinement
HKL-2000data scaling
SCALEPACKdata scaling
RESOLVEphasing
HKL-2000data reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

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