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- PDB-2o4m: Structure of Phosphotriesterase mutant I106G/F132G/H257Y -

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Basic information

Entry
Database: PDB / ID: 2o4m
TitleStructure of Phosphotriesterase mutant I106G/F132G/H257Y
ComponentsParathion hydrolase
KeywordsHYDROLASE / METALLOENZYME / TIM BARREL / NERVE AGENTS
Function / homology
Function and homology information


aryldialkylphosphatase / aryldialkylphosphatase activity / catabolic process / zinc ion binding / plasma membrane
Similarity search - Function
Aryldialkylphosphatase, zinc-binding site / Phosphotriesterase family signature 1. / Phosphotriesterase / Phosphotriesterase family / Phosphotriesterase family profile. / Metal-dependent hydrolases / Metal-dependent hydrolase / Twin arginine translocation (Tat) signal profile. / Twin-arginine translocation pathway, signal sequence / TIM Barrel ...Aryldialkylphosphatase, zinc-binding site / Phosphotriesterase family signature 1. / Phosphotriesterase / Phosphotriesterase family / Phosphotriesterase family profile. / Metal-dependent hydrolases / Metal-dependent hydrolase / Twin arginine translocation (Tat) signal profile. / Twin-arginine translocation pathway, signal sequence / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
ACETIC ACID / CACODYLATE ION / Parathion hydrolase
Similarity search - Component
Biological speciesBrevundimonas diminuta (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.64 Å
AuthorsKim, J. / Ramagopal, U.A. / Tsai, P. / Raushel, F.M. / Almo, S.C.
CitationJournal: To be Published
Title: Structure of Phosphotriesterase mutant I106G/F132G/H257Y
Authors: Kim, J. / Ramagopal, U.A. / Tsai, P. / Raushel, F.M. / Almo, S.C.
History
DepositionDec 4, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 18, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.2Oct 18, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.3Oct 20, 2021Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / 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_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_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_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.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 1.4Aug 30, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Parathion hydrolase
B: Parathion hydrolase
C: Parathion hydrolase
P: Parathion hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)145,92839
Polymers143,2354
Non-polymers2,69335
Water28,7161594
1
A: Parathion hydrolase
B: Parathion hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,82318
Polymers71,6172
Non-polymers1,20616
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: Parathion hydrolase
P: Parathion hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,10521
Polymers71,6172
Non-polymers1,48719
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)56.759, 68.906, 89.670
Angle α, β, γ (deg.)90.03, 100.29, 94.12
Int Tables number1
Space group name H-MP1

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Components

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Protein , 1 types, 4 molecules ABCP

#1: Protein
Parathion hydrolase / Phosphotriesterase / PTE


Mass: 35808.734 Da / Num. of mol.: 4 / Fragment: residues 34-364 / Mutation: I106G, F132G, H257Y
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Brevundimonas diminuta (bacteria) / Gene: opd / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P0A434, aryldialkylphosphatase

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Non-polymers , 5 types, 1629 molecules

#2: Chemical...
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 23 / Source method: obtained synthetically / Formula: Zn
#3: Chemical
ChemComp-CAC / CACODYLATE ION / dimethylarsinate / Cacodylic acid


Mass: 136.989 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6AsO2
#4: Chemical ChemComp-ACY / ACETIC ACID / Acetic acid


Mass: 60.052 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H4O2
#5: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1594 / Source method: isolated from a natural source / Formula: H2O

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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: 2.4 Å3/Da / Density % sol: 48.81 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: Zinc acetate 0.2 M, Sodium Cacodylate 0.1 M, PEG MME 12 %, pH 6.5, Vapor diffusion, Hanging drop, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X6A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Jul 19, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.58→28.33 Å / Num. all: 169088 / Num. obs: 169088 / % possible obs: 93.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 1.9 % / Rmerge(I) obs: 0.075 / Rsym value: 0.06 / Χ2: 1.144 / Net I/σ(I): 8.4
Reflection shellResolution: 1.58→1.64 Å / Redundancy: 1.7 % / Rmerge(I) obs: 0.397 / Mean I/σ(I) obs: 1.53 / Num. unique all: 13353 / Rsym value: 0.334 / Χ2: 0.844 / % possible all: 73.5

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACT2data extraction
ADSCQuantumdata collection
HKL-2000data reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1P6B

1p6b


Resolution: 1.64→28.33 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.927 / SU B: 2.211 / SU ML: 0.078 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.111 / ESU R Free: 0.118 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.244 7763 5 %RANDOM
Rwork0.189 ---
all0.192 ---
obs0.192 155682 95.27 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 19.873 Å2
Baniso -1Baniso -2Baniso -3
1-1.25 Å2-0.03 Å2-0.21 Å2
2---0.6 Å2-0.07 Å2
3----0.72 Å2
Refinement stepCycle: LAST / Resolution: 1.64→28.33 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10075 0 85 1594 11754
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.02210549
X-RAY DIFFRACTIONr_angle_refined_deg1.561.96714358
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.14751385
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.11422.132441
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.129151713
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.30215113
X-RAY DIFFRACTIONr_chiral_restr0.3020.21660
X-RAY DIFFRACTIONr_gen_planes_refined0.0180.028005
X-RAY DIFFRACTIONr_nbd_refined0.2220.25822
X-RAY DIFFRACTIONr_nbtor_refined0.3180.27415
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1590.21292
X-RAY DIFFRACTIONr_metal_ion_refined0.0860.227
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2750.276
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1930.255
X-RAY DIFFRACTIONr_mcbond_it1.8791.56839
X-RAY DIFFRACTIONr_mcangle_it2.452210783
X-RAY DIFFRACTIONr_scbond_it3.84934113
X-RAY DIFFRACTIONr_scangle_it5.4534.53554
LS refinement shellResolution: 1.64→1.683 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.321 561 -
Rwork0.255 10795 -
obs-11356 93.86 %

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