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- PDB-3h7k: Crystal Structure of Arabidopsis thaliana Agmatine Deiminase Comp... -

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Basic information

Entry
Database: PDB / ID: 3h7k
TitleCrystal Structure of Arabidopsis thaliana Agmatine Deiminase Complexed with a Covalently Bound Reaction Intermediate
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
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.84 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 27, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 26, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Aug 10, 2011Group: Non-polymer description
Revision 1.3Aug 17, 2011Group: Structure summary
Revision 1.4Nov 1, 2017Group: Refinement description / Category: software
Revision 1.5Mar 26, 2025Group: 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 / pdbx_struct_conn_angle / 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 / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_alt_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_alt_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _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
A: Agmatine deiminase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,9839
Polymers43,5461
Non-polymers4388
Water4,558253
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)123.720, 69.560, 50.986
Angle α, β, γ (deg.)90.000, 98.520, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-526-

HOH

21A-588-

HOH

Detailsbiological unit is the same as asymmetric unit.

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Components

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Protein , 1 types, 1 molecules A

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


Mass: 43545.582 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
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 , 5 types, 261 molecules

#2: Chemical ChemComp-MG / MAGNESIUM ION


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


Mass: 22.990 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Na
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#5: Chemical ChemComp-1PE / PENTAETHYLENE GLYCOL / PEG400


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


Mass: 18.015 Da / Num. of mol.: 253 / 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: 2.49 Å3/Da / Density % sol: 50.63 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: Protein solution 100 nl- 10 mg/ml agmatine deiminase, 50 mM NaCl, 0.3 mM TCEP, 10 mM agmatine sulfate, 5 mM HEPES, pH 7.0; Precipitant solution 100 nl- 32% Polyethylene glycol 1500, 200 mM ...Details: Protein solution 100 nl- 10 mg/ml agmatine deiminase, 50 mM NaCl, 0.3 mM TCEP, 10 mM agmatine sulfate, 5 mM HEPES, pH 7.0; Precipitant solution 100 nl- 32% Polyethylene glycol 1500, 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: 0.97942 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Apr 6, 2009
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97942 Å / Relative weight: 1
ReflectionRedundancy: 7.3 % / Av σ(I) over netI: 25.03 / Number: 272339 / Rmerge(I) obs: 0.094 / Χ2: 1.62 / D res high: 1.84 Å / D res low: 50 Å / Num. obs: 37121 / % possible obs: 100
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsChi squaredRedundancy
4.995010010.0674.2437.5
3.964.9910010.0522.8257.7
3.463.9610010.0582.2387.7
3.153.4610010.072.1667.6
2.923.1510010.0792.1737.6
2.752.9210010.0871.9527.6
2.612.7510010.0981.47.5
2.52.6110010.1081.4897.5
2.42.510010.1121.1847.4
2.322.410010.1171.2797.4
2.252.3210010.1231.1797.5
2.182.2510010.1371.1777.4
2.122.1810010.1461.117.4
2.072.1210010.1611.1187.4
2.032.0710010.1761.1127.3
1.982.0310010.1981.1017.3
1.941.9899.910.2351.057.2
1.911.9410010.2591.0947.1
1.871.9110010.2891.0086.6
1.841.8799.810.3051.0256
ReflectionResolution: 1.84→50 Å / Num. obs: 37121 / % possible obs: 100 % / Redundancy: 7.3 % / Rmerge(I) obs: 0.094 / Χ2: 1.623 / Net I/σ(I): 25.028
Reflection shellResolution: 1.84→1.87 Å / Redundancy: 6 % / Rmerge(I) obs: 0.305 / Mean I/σ(I) obs: 5.647 / Num. unique all: 1870 / Χ2: 1.025 / % possible all: 99.8

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Phasing

PhasingMethod: SAD
Phasing MAD set
IDHighest resolution (Å)Lowest resolution (Å)Power acentricPower centricReflection acentricReflection centric
ISO_11.8440.200356531441
ANO_11.8440.21.930355930
Phasing MAD set shell
IDResolution (Å)Power acentricPower centricReflection acentricReflection centric
ISO_18.07-40.20039673
ISO_15.77-8.070071568
ISO_14.72-5.770093974
ISO_14.1-4.7200109972
ISO_13.67-4.100127573
ISO_13.35-3.6700139374
ISO_13.1-3.3500153269
ISO_12.91-3.100163078
ISO_12.74-2.9100174570
ISO_12.6-2.7400185669
ISO_12.48-2.600193071
ISO_12.37-2.4800203078
ISO_12.28-2.3700211971
ISO_12.2-2.2800221970
ISO_12.12-2.200227971
ISO_12.06-2.1200234472
ISO_12-2.0600246772
ISO_11.94-200251578
ISO_11.89-1.9400257565
ISO_11.84-1.8900259573
ANO_18.07-40.26.34203960
ANO_15.77-8.076.16507150
ANO_14.72-5.775.22909390
ANO_14.1-4.724.449010990
ANO_13.67-4.13.917012750
ANO_13.35-3.673.617013930
ANO_13.1-3.353.664015320
ANO_12.91-3.13.528016300
ANO_12.74-2.913.15017440
ANO_12.6-2.742.566018550
ANO_12.48-2.62.318019270
ANO_12.37-2.482.032020300
ANO_12.28-2.371.9021160
ANO_12.2-2.281.708022160
ANO_12.12-2.21.499022740
ANO_12.06-2.121.41023440
ANO_12-2.061.268024640
ANO_11.94-21.123025140
ANO_11.89-1.941.008025680
ANO_11.84-1.890.913025620
Phasing MAD set site
IDCartn x (Å)Cartn y (Å)Cartn z (Å)Atom type symbolB isoOccupancy
1-14.136-8.417-0.803SE13.031.84
2-37.702-18.193-14.644SE9.641.54
3-28.3437.511-1.522SE11.11.38
4-52.81337.086-16.684SE12.821.27
5-30.45543.07-20.45SE19.510.85
6-27.32940.046-21.514SE16.640.85
7-52.204-28.477-21.616SE12.560.7

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
SHARPphasing
SOLOMONphasing
REFMACrefmac_5.5.0066refinement
PDB_EXTRACT3.005data extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: SAD / Resolution: 1.84→40.2 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.939 / Occupancy max: 1 / Occupancy min: 0.3 / SU B: 1.796 / SU ML: 0.057 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.106 / ESU R Free: 0.106 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.185 1849 5 %RANDOM
Rwork0.147 ---
obs0.149 37094 99.7 %-
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: 55.22 Å2 / Biso mean: 12.976 Å2 / Biso min: 2 Å2
Baniso -1Baniso -2Baniso -3
1--0.35 Å20 Å2-0.25 Å2
2--0.44 Å20 Å2
3----0.17 Å2
Refinement stepCycle: LAST / Resolution: 1.84→40.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2921 0 20 253 3194
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0213102
X-RAY DIFFRACTIONr_angle_refined_deg1.3611.9424223
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.85387
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.51524.129155
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.54415502
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.5291524
X-RAY DIFFRACTIONr_chiral_restr0.1240.2444
X-RAY DIFFRACTIONr_gen_planes_refined0.0160.0212449
X-RAY DIFFRACTIONr_mcbond_it1.5591.51897
X-RAY DIFFRACTIONr_mcangle_it2.42623076
X-RAY DIFFRACTIONr_scbond_it3.86931205
X-RAY DIFFRACTIONr_scangle_it6.1194.51147
LS refinement shellResolution: 1.84→1.888 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.202 149 -
Rwork0.174 2517 -
all-2666 -
obs--96.95 %

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