3H7K

Crystal Structure of Arabidopsis thaliana Agmatine Deiminase Complexed with a Covalently Bound Reaction Intermediate


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.84 Å
  • R-Value Free: 0.185 
  • R-Value Work: 0.147 

wwPDB Validation 3D Report Full Report


This is version 1.4 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
A
383Arabidopsis thalianaMutation(s): 0 
Gene Names: AIH (EMB1873)
EC: 3.5.3.12
Find proteins for Q8GWW7 (Arabidopsis thaliana)
Go to UniProtKB:  Q8GWW7
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NA
Query on NA

Download SDF File 
Download CCD File 
A
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
CL
Query on CL

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Download CCD File 
A
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
MG
Query on MG

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Download CCD File 
A
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
1PE
Query on 1PE

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Download CCD File 
A
PENTAETHYLENE GLYCOL
PEG400
C10 H22 O6
JLFNLZLINWHATN-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  2 Unique
IDChainsTypeFormula2D DiagramParent
MSE
Query on MSE
A
L-PEPTIDE LINKINGC5 H11 N O2 SeMET
AGT
Query on AGT
A
L-PEPTIDE LINKINGC8 H20 N4 O2 SCYS
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.84 Å
  • R-Value Free: 0.185 
  • R-Value Work: 0.147 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 123.720α = 90.00
b = 69.560β = 98.52
c = 50.986γ = 90.00
Software Package:
Software NamePurpose
SCALEPACKdata scaling
HKL-2000data collection
DENZOdata reduction
SOLOMONphasing
HKL-2000data reduction
REFMACrefinement
PDB_EXTRACTdata extraction
SHARPphasing
HKL-2000data scaling

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: 2011-08-10
    Type: Non-polymer description
  • Version 1.3: 2011-08-17
    Type: Structure summary
  • Version 1.4: 2017-11-01
    Type: Refinement description