3H7C | pdb_00003h7c

Crystal Structure of Arabidopsis thaliana Agmatine Deiminase from Cell Free Expression

• PDB DOI: https://doi.org/10.2210/pdb3H7C/pdb

• Classification: HYDROLASE
• Organism(s): Arabidopsis thaliana
• Mutation(s): No 


• Deposited: 2009-04-24 Released: 2009-05-26 
• Deposition Author(s): Burgie, E.S., Bingman, C.A., Phillips Jr., G.N., Center for Eukaryotic Structural Genomics (CESG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.50 Å
• R-Value Free: 
  0.174 (Depositor), 0.169 (DCC) 
• R-Value Work: 
  0.146 (Depositor), 0.149 (DCC) 
• R-Value Observed: 
  0.147 (Depositor) 

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.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 44 kDa 
• Atom Count: 3,475 
• Modeled Residue Count: 369 
• Deposited Residue Count: 383 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Agmatine deiminase	A [auth X]	383	Arabidopsis thaliana	Mutation(s): 0  Gene Names: AIH, At5g08170, EMB1873, T22D6.110 EC: 3.5.3.12
UniProt
Find proteins for Q8GWW7 (Arabidopsis thaliana) Explore Q8GWW7  Go to UniProtKB:  Q8GWW7

Small Molecules

Ligands 6 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
1PE	I [auth X]	PENTAETHYLENE GLYCOL C10 H22 O6 JLFNLZLINWHATN-UHFFFAOYSA-N
211	H [auth X]	2,2',2''-NITRILOTRIETHANOL C6 H15 N O3 GSEJCLTVZPLZKY-UHFFFAOYSA-N
K	G [auth X]	POTASSIUM ION K NPYPAHLBTDXSSS-UHFFFAOYSA-N
CL	B [auth X], C [auth X]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M
MG	D [auth X]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N
NA	E [auth X], F [auth X]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A [auth X]	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.50 Å
• R-Value Free:  0.174 (Depositor), 0.169 (DCC) 
• R-Value Work:  0.146 (Depositor), 0.149 (DCC) 
• R-Value Observed: 0.147 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 123.715	α = 90
b = 69.932	β = 98.4
c = 50.917	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
RESOLVE	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-2000	data collection
HKL-2000	data reduction
HKL-2000	data scaling
AutoSol	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2009-05-26 
Deposition Author(s): Burgie, E.S., Bingman, C.A., Phillips Jr., G.N., Center for Eukaryotic Structural Genomics (CESG)

Revision History  

• 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
• Version 1.3: 2024-11-06
  Changes: Data collection, Database references, Derived calculations, Structure summary