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Basic information

Entry
Database: PDB / ID: 2q3u
TitleEnsemble refinement of the protein crystal structure of gene product from Arabidopsis thaliana At5g08170, agmatine iminohydrolase
ComponentsAgmatine deiminase
KeywordsHYDROLASE / Ensemble Refinement / Refinement Methodology Development / At5g08170 / POLYAMINE BIOSYNTHESIS / AGMATINE IMINOHYDROLASE / AIH / AGMATINE DEIMINASE / N-CARBAMOYLPUTRESCINE / PUTRESCINE / Structural Genomics / Protein Structure Initiative / PSI / Center for Eukaryotic Structural Genomics / CESG
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 / Re-refinement using ensemble model / Resolution: 1.53 Å
AuthorsLevin, E.J. / Kondrashov, D.A. / Wesenberg, G.E. / Phillips Jr., G.N. / Center for Eukaryotic Structural Genomics (CESG)
CitationJournal: Structure / Year: 2007
Title: Ensemble refinement of protein crystal structures: validation and application.
Authors: Levin, E.J. / Kondrashov, D.A. / Wesenberg, G.E. / Phillips, G.N.
History
DepositionMay 30, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 19, 2007Provider: repository / Type: Initial release
Revision 1.1Sep 25, 2007Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 10, 2011Group: Other
Revision 1.4Aug 30, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_conn_type / 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_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_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_asym_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_conn.ptnr2_label_seq_id / _struct_conn_type.id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2
Remark 300 BIOMOLECULE: 1,2 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 2 ... BIOMOLECULE: 1,2 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 2 CHAIN(S). AUTHORS STATE THAT THE BIOLOGICAL UNIT OF THIS PROTEIN IS UNKNOWN.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Agmatine deiminase
B: Agmatine deiminase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)88,10818
Polymers87,0432
Non-polymers1,06516
Water14,034779
1
A: Agmatine deiminase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,18910
Polymers43,5211
Non-polymers6689
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Agmatine deiminase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,9188
Polymers43,5211
Non-polymers3977
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)58.020, 115.813, 66.634
Angle α, β, γ (deg.)90.000, 97.100, 90.000
Int Tables number4
Space group name H-MP1211
Number of models8

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Components

#1: Protein Agmatine deiminase / Agmatine iminohydrolase


Mass: 43521.414 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Strain: cv. Columbia / Gene: AIH, At5g08170, T22D6.110 / Plasmid: PVP13 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta / References: UniProt: Q8GWW7, agmatine deiminase
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-MPO / 3[N-MORPHOLINO]PROPANE SULFONIC ACID


Mass: 209.263 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H15NO4S / Comment: pH buffer*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 779 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.55 Å3/Da / Density % sol: 51.78 % / Description: AUTHOR USED THE SF DATA FROM ENTRY 1VKP.

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Data collection

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1

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Processing

Software
NameVersionClassificationNB
CNS1.1refinement
PDB_EXTRACT2data extraction
CNS1.1phasing
RefinementMethod to determine structure: Re-refinement using ensemble model
Starting model: PDB entry 1VKP

1vkp


Resolution: 1.53→19.87 Å / Rfactor Rfree error: 0.002 / Data cutoff high absF: 1582981.25 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
Stereochemistry target values: maximum likelihood using amplitudes
Details: This PDB entry is a re-refinement using an ensemble model of the previously deposited single-conformer structure 1vkp and the first data set in the deposited structure factor file for 1vkp ...Details: This PDB entry is a re-refinement using an ensemble model of the previously deposited single-conformer structure 1vkp and the first data set in the deposited structure factor file for 1vkp along with the R-free set defined therein. The coordinates were generated by an automated protocol from an initial model consisting of 8 identical copies of the protein and non-water hetero-atoms assigned fractional occupancies adding up to one, and a single copy of the solvent molecules. Refinement was carried out with all the conformers present simultaneously and with the potential energy terms corresponding to interactions between the different conformers excluded. The helix and sheet records were calculated using coordinates from the first conformer only. The structure visualization program PYMOL is well-suited for directly viewing the ensemble model presented in this PDB file.
RfactorNum. reflection% reflectionSelection details
Rfree0.171 6038 5 %RANDOM
Rwork0.135 ---
obs0.135 119958 91.8 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 55.425 Å2 / ksol: 0.381 e/Å3
Displacement parametersBiso mean: 18.3 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.14 Å0.1 Å
Luzzati d res low-5 Å
Luzzati sigma a0.03 Å-0.05 Å
Refinement stepCycle: LAST / Resolution: 1.53→19.87 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5784 0 67 779 6630
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.036
X-RAY DIFFRACTIONc_angle_deg2.7
X-RAY DIFFRACTIONc_dihedral_angle_d24.6
X-RAY DIFFRACTIONc_improper_angle_d1.97
X-RAY DIFFRACTIONc_mcbond_it1.411.5
X-RAY DIFFRACTIONc_mcangle_it2.032
X-RAY DIFFRACTIONc_scbond_it2.52
X-RAY DIFFRACTIONc_scangle_it3.532.5
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 6

Resolution (Å)Rfactor RfreeNum. reflection Rfree% reflection Rfree (%)Rfactor RworkNum. reflection RworkRfactor Rfree errorNum. reflection allNum. reflection obs% reflection obs (%)
1.53-1.630.1768785.20.119158750.006217111675377.2
1.63-1.750.1619705.10.104178820.005217651885286.6
1.75-1.930.161100850.106190250.005217092003392.3
1.93-2.210.16810434.90.13200520.005217252109597.1
2.21-2.780.16910484.90.125203820.005217922143098.3
2.78-19.870.177109150.155207040.005219292179599.4
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater.top
X-RAY DIFFRACTION3ion.param
X-RAY DIFFRACTION4mpo_xplor_par.txt
X-RAY DIFFRACTION5edo.param

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