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- PDB-3h7c: Crystal Structure of Arabidopsis thaliana Agmatine Deiminase from... -

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Basic information

Entry
Database: PDB / ID: 3h7c
TitleCrystal Structure of Arabidopsis thaliana Agmatine Deiminase from Cell Free Expression
ComponentsAgmatine deiminase
KeywordsHYDROLASE / Agmatine / Structural Genomics / Protein Structure Initiative / PSI / Center for Eukaryotic Structural Genomics / CESG / N-carbamoylputrescine / Arginine decarboxylase pathway / Polyamine biosynthesis
Function / homology
Function and homology information


agmatine deiminase / agmatine deiminase activity / putrescine biosynthetic process from arginine / polyamine biosynthetic process / protein-arginine deiminase activity
Similarity search - Function
Agmatine deiminase / Peptidyl-arginine deiminase, Porphyromonas-type / Porphyromonas-type peptidyl-arginine deiminase / L-arginine/glycine Amidinotransferase; Chain A / 5-stranded Propeller / L-arginine/glycine Amidinotransferase; Chain A / Alpha Beta
Similarity search - Domain/homology
2,2',2''-NITRILOTRIETHANOL / : / Agmatine deiminase
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.5 Å
AuthorsBurgie, E.S. / Bingman, C.A. / Phillips Jr., G.N. / Center for Eukaryotic Structural Genomics (CESG)
CitationJournal: To be Published
Title: Structural Insights into the Catalytic Mechanism of Arabidopsis thaliana Agmatine Deiminase
Authors: Burgie, E.S. / Bingman, C.A. / Phillips Jr., G.N.
History
DepositionApr 24, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 26, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software
Revision 1.3Nov 6, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_entry_details.has_protein_modification / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
X: Agmatine deiminase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,9989
Polymers43,4301
Non-polymers5688
Water6,521362
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)123.715, 69.932, 50.917
Angle α, β, γ (deg.)90.000, 98.400, 90.000
Int Tables number5
Space group name H-MC121
Detailsbiological unit is the same as asymmetric unit.

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Components

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Protein , 1 types, 1 molecules X

#1: Protein Agmatine deiminase / Agmatine iminohydrolase / Protein EMBRYO DEFECTIVE 1873


Mass: 43430.402 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: Cell free synthesis / Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Strain: Columbia / Description: Wheat germ / Gene: AIH, At5g08170, EMB1873, T22D6.110 / Plasmid: pEU-His-Flexi / Production host: CELL-FREE SYNTHESIS (others) / References: UniProt: Q8GWW7, agmatine deiminase

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Non-polymers , 7 types, 370 molecules

#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#5: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: K
#6: Chemical ChemComp-211 / 2,2',2''-NITRILOTRIETHANOL


Mass: 149.188 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H15NO3
#7: Chemical ChemComp-1PE / PENTAETHYLENE GLYCOL / PEG400


Mass: 238.278 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H22O6 / Comment: precipitant*YM
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 362 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY
Sequence detailsAUTHORS STATE THAT THE SEQUENCE MATCHES GENBANK ENTRY AAO63405.1. THE DISCREPANCY BETWEEN AUTHOR'S ...AUTHORS STATE THAT THE SEQUENCE MATCHES GENBANK ENTRY AAO63405.1. THE DISCREPANCY BETWEEN AUTHOR'S SEQUENCE AND THE SEQUENCE LISTED IN UNIPROT IS A KNOWN "SEQUENCE CONFLICT". THIS IS DOCUMENTED ON THE UNIPROT WEBSITE AT HTTP://WWW.UNIPROT.ORG/UNIPROT/Q8GWW7. AT THE WEBSITE TWO INDEPENDENT REFERENCES ARE PROVIDED. FURTHERMORE, AUTHOR'S ELECTRON DENSITY SHOWS NO SIGN OF ASPARTATE AT THIS POSITION. THIS SEQUENCE IS LIKELY JUST A NATURAL VARIATION, AND WAS NOT PRODUCED BY SITE-DIRECTED MUTAGENSIS.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.51 Å3/Da / Density % sol: 50.97 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: Protein solution- 10 mg/ml agmatine deiminase, 50 mM NaCl, 0.3 mM TCEP, 5 mM HEPES, pH 7.0; Precipitant solution- 34% Polyethylene glycol 2000, 200 mM KBr, 100 mM triethanolamine, pH 7.5; ...Details: Protein solution- 10 mg/ml agmatine deiminase, 50 mM NaCl, 0.3 mM TCEP, 5 mM HEPES, pH 7.0; Precipitant solution- 34% Polyethylene glycol 2000, 200 mM KBr, 100 mM triethanolamine, pH 7.5; Cryoprotectant- MiTeGen LV Cryo Oil, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 0.96350,0.97943,0.97957
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Apr 6, 2009
RadiationMonochromator: Si(111) / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.96351
20.979431
30.979571
ReflectionResolution: 1.5→50 Å / Num. all: 68398 / Num. obs: 68398 / % possible obs: 100 % / Redundancy: 7.5 % / Rmerge(I) obs: 0.098 / Net I/σ(I): 19.6
Reflection shellResolution: 1.5→1.53 Å / Redundancy: 6.7 % / Rmerge(I) obs: 0.444 / Mean I/σ(I) obs: 4.1 / Num. unique all: 3395 / % possible all: 100

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
RESOLVEphasing
REFMAC5.5.0066refinement
PDB_EXTRACT3.005data extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
AutoSolphasing
RefinementMethod to determine structure: MAD / Resolution: 1.5→50 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.955 / Occupancy max: 1 / Occupancy min: 0.2 / SU B: 0.884 / SU ML: 0.034 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.058 / ESU R Free: 0.062 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.174 3460 5.1 %RANDOM
Rwork0.146 ---
obs0.147 68375 99.75 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso max: 71.57 Å2 / Biso mean: 14.686 Å2 / Biso min: 2 Å2
Baniso -1Baniso -2Baniso -3
1--0.41 Å20 Å2-0.37 Å2
2--0.65 Å20 Å2
3----0.34 Å2
Refinement stepCycle: LAST / Resolution: 1.5→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3073 0 30 372 3475
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0213187
X-RAY DIFFRACTIONr_angle_refined_deg1.631.9394347
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.0445405
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.77724.099161
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.18415520
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.2891526
X-RAY DIFFRACTIONr_chiral_restr0.1310.2450
X-RAY DIFFRACTIONr_gen_planes_refined0.0180.0212547
X-RAY DIFFRACTIONr_mcbond_it1.5411.51950
X-RAY DIFFRACTIONr_mcangle_it2.51923170
X-RAY DIFFRACTIONr_scbond_it3.59831237
X-RAY DIFFRACTIONr_scangle_it5.6774.51177
LS refinement shellResolution: 1.501→1.54 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.24 225 -
Rwork0.21 4702 -
all-4927 -
obs--96.97 %

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