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- PDB-2o4q: Structure of Phosphotriesterase mutant G60A -

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Basic information

Entry
Database: PDB / ID: 2o4q
TitleStructure of Phosphotriesterase mutant G60A
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
CACODYLATE ION / Parathion hydrolase
Similarity search - Component
Biological speciesBrevundimonas diminuta (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
AuthorsKim, J. / Ramagopal, U.A. / Tsai, P.C. / Raushel, F.M. / Almo, S.C.
CitationJournal: Biochemistry / Year: 2008
Title: Structure of diethyl phosphate bound to the binuclear metal center of phosphotriesterase.
Authors: Kim, J. / Tsai, P.C. / Chen, S.L. / Himo, F. / Almo, S.C. / Raushel, F.M.
History
DepositionDec 4, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 18, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Derived calculations / 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

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)144,84716
Polymers143,7764
Non-polymers1,07112
Water18,4831026
1
A: Parathion hydrolase
B: Parathion hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,4248
Polymers71,8882
Non-polymers5366
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3660 Å2
ΔGint-159 kcal/mol
Surface area23170 Å2
MethodPISA, PQS
2
K: Parathion hydrolase
P: Parathion hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,4248
Polymers71,8882
Non-polymers5366
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3650 Å2
ΔGint-161 kcal/mol
Surface area23190 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)55.295, 68.299, 90.030
Angle α, β, γ (deg.)90.05, 100.42, 89.96
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
Parathion hydrolase / Phosphotriesterase / PTE


Mass: 35943.961 Da / Num. of mol.: 4 / Fragment: residues 34-364 / Mutation: G60A
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
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Zn
#3: Chemical
ChemComp-CAC / CACODYLATE ION / dimethylarsinate


Mass: 136.989 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6AsO2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1026 / 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: 2.33 Å3/Da / Density % sol: 47.12 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.2M Mg acetate, 0.1M Na-cacodylate, 20% PEG 8000, 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: X3A / Wavelength: 0.97904 Å
DetectorType: MAR CCD 165 mm / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97904 Å / Relative weight: 1
ReflectionResolution: 1.95→31.64 Å / Num. all: 91515 / Num. obs: 91515 / % possible obs: 96.3 % / Observed criterion σ(I): 0 / Redundancy: 3 % / Rmerge(I) obs: 0.076 / Rsym value: 0.072 / Χ2: 1.127 / Net I/σ(I): 7.7
Reflection shellResolution: 1.95→2.02 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.242 / Mean I/σ(I) obs: 3.39 / Num. unique all: 7663 / Rsym value: 0.286 / Χ2: 0.843 / % possible all: 80.7

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMAC5.2.0019refinement
PDB_EXTRACT2data extraction
HKL-2000data reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1p6b

1p6b


Resolution: 1.95→31.64 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.924 / SU B: 3.626 / SU ML: 0.106 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.17 / ESU R Free: 0.163 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.226 4597 5 %RANDOM
Rwork0.164 ---
obs0.168 91514 97.09 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 21.737 Å2
Baniso -1Baniso -2Baniso -3
1-1.94 Å20.03 Å20.25 Å2
2---0.9 Å2-0.6 Å2
3----0.95 Å2
Refinement stepCycle: LAST / Resolution: 1.95→31.64 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10110 0 28 1026 11164
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.02210377
X-RAY DIFFRACTIONr_angle_refined_deg1.4241.96314109
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.40951334
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.18322.333433
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.812151677
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.10315104
X-RAY DIFFRACTIONr_chiral_restr0.120.21646
X-RAY DIFFRACTIONr_gen_planes_refined0.0170.027840
X-RAY DIFFRACTIONr_nbd_refined0.2190.25387
X-RAY DIFFRACTIONr_nbtor_refined0.3160.27286
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1530.21001
X-RAY DIFFRACTIONr_metal_ion_refined0.0470.210
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2080.266
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1540.227
X-RAY DIFFRACTIONr_mcbond_it1.8251.56774
X-RAY DIFFRACTIONr_mcangle_it2.503210637
X-RAY DIFFRACTIONr_scbond_it4.14534018
X-RAY DIFFRACTIONr_scangle_it5.9784.53472
LS refinement shellResolution: 1.95→2.002 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.277 291 -
Rwork0.179 5644 -
obs-5935 85.18 %

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