3H7K

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

PDB DOI: https://doi.org/10.2210/pdb3H7K/pdb

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

Deposited: 2009-04-27 Released: 2009-05-26
Deposition Author(s): Burgie, E.S., Bingman, C.A., Phillips Jr., G.N., Center for Eukaryotic Structural Genomics (CESG)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.84 Å
R-Value Free: 0.185
R-Value Work: 0.147
R-Value Observed: 0.149

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.

Macromolecule Content

Total Structure Weight: 43.98 kDa
Atom Count: 3,281
Modelled Residue Count: 367
Deposited Residue Count: 383
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Agmatine deiminase	A	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
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q8GWW7
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
1PE Query on 1PE Download Ideal Coordinates CCD File SDF format, chain I [auth A] MOL2 format, chain I [auth A] mmCIF format, chain I [auth A]	I [auth A]	PENTAETHYLENE GLYCOL C₁₀ H₂₂ O₆ JLFNLZLINWHATN-UHFFFAOYSA-N		Interactions Focus chain I [auth A]
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain G [auth A] SDF format, chain H [auth A] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] mmCIF format, chain F [auth A] mmCIF format, chain G [auth A] mmCIF format, chain H [auth A]	F [auth A], G [auth A], H [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A]
MG Query on MG Download Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain B [auth A]
NA Query on NA Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain D [auth A] SDF format, chain E [auth A] MOL2 format, chain C [auth A] MOL2 format, chain D [auth A] MOL2 format, chain E [auth A] mmCIF format, chain C [auth A] mmCIF format, chain D [auth A] mmCIF format, chain E [auth A]	C [auth A], D [auth A], E [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A]

Modified Residues 2 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
AGT Query on AGT	A	L-PEPTIDE LINKING	C₈ H₂₀ N₄ O₂ S		CYS
MSE Query on MSE	A	L-PEPTIDE LINKING	C₅ H₁₁ N O₂ Se		MET

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.84 Å
R-Value Free: 0.185
R-Value Work: 0.147
R-Value Observed: 0.149
Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 123.72	α = 90
b = 69.56	β = 98.52
c = 50.986	γ = 90

Software Package:

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