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- PDB-3a3w: Structure of OpdA mutant (G60A/A80V/S92A/R118Q/K185R/Q206P/D208G/... -

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Basic information

Entry
Database: PDB / ID: 3a3w
TitleStructure of OpdA mutant (G60A/A80V/S92A/R118Q/K185R/Q206P/D208G/I260T/G273S) with diethyl 4-methoxyphenyl phosphate bound in the active site
ComponentsPhosphotriesterase
KeywordsHYDROLASE / phosphotriesterase / OPDA / metalloenzyme
Function / homology
Function and homology information


hydrolase activity, acting on ester bonds / catabolic process / zinc ion binding
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 / Prokaryotic membrane lipoprotein lipid attachment site profile. ...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 / Prokaryotic membrane lipoprotein lipid attachment site profile. / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
: / DIETHYL 4-METHOXYPHENYL PHOSPHATE / Phosphotriesterase
Similarity search - Component
Biological speciesAgrobacterium tumefaciens (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 Å
AuthorsOllis, D.L. / Tawfik, D.S. / Schenk, G. / Jackson, C.J. / Foo, J.L. / Tokuriki, N. / Afriat, L. / Carr, P.D. / Kim, H.K.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2009
Title: Conformational sampling, catalysis, and evolution of the bacterial phosphotriesterase
Authors: Jackson, C.J. / Foo, J.-L. / Tokuriki, N. / Afriat, L. / Carr, P.D. / Kim, H.-K. / Schenk, G. / Tawfik, D.S. / Ollis, D.L.
History
DepositionJun 23, 2009Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 12, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 10, 2021Group: Database references / Derived calculations
Category: database_2 / struct_conn ...database_2 / 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 / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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.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
Revision 1.3Nov 1, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.4Nov 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: Phosphotriesterase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,0224
Polymers35,6441
Non-polymers3783
Water5,098283
1
A: Phosphotriesterase
hetero molecules

A: Phosphotriesterase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,0438
Polymers71,2872
Non-polymers7566
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555y,x,-z1
Buried area4850 Å2
ΔGint-47 kcal/mol
Surface area22320 Å2
MethodPISA
Unit cell
Length a, b, c (Å)109.011, 109.011, 62.689
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein Phosphotriesterase


Mass: 35643.582 Da / Num. of mol.: 1 / Fragment: UNP residues 32-360
Mutation: G60A, A80V, S92A, R118Q, K185R, Q206P, D208G, I260T, G273S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Agrobacterium tumefaciens (bacteria) / Gene: opdA / Plasmid: pETMCSI / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)recA- / References: UniProt: Q93LD7, aryldialkylphosphatase
#2: Chemical ChemComp-CO / COBALT (II) ION


Mass: 58.933 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Co
#3: Chemical ChemComp-EPL / DIETHYL 4-METHOXYPHENYL PHOSPHATE


Mass: 260.223 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H17O5P
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 283 / 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: 3.02 Å3/Da / Density % sol: 59.23 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 20% PEG3350, 0.2M NaNO3, pH7, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.975 Å
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Nov 13, 2007
Details: flat collimating mirror, double crystal monochromator, toroid focusing mirror
RadiationMonochromator: Double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.975 Å / Relative weight: 1
ReflectionResolution: 1.7→40 Å / Num. all: 43843 / Num. obs: 43843 / % possible obs: 92.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shellResolution: 1.7→1.76 Å / % possible all: 51.9

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Processing

Software
NameVersionClassification
REFMAC5.5.0088refinement
CrystalCleardata collection
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2D2J

2d2j


Resolution: 1.85→29.8 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.945 / SU B: 2.976 / SU ML: 0.088 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.113 / ESU R Free: 0.112 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20883 1715 4.7 %RANDOM
Rwork0.17404 ---
obs0.17569 34885 99.21 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 25 Å2
Baniso -1Baniso -2Baniso -3
1--1.31 Å2-0.65 Å20 Å2
2---1.31 Å20 Å2
3---1.96 Å2
Refinement stepCycle: LAST / Resolution: 1.85→29.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2520 0 19 283 2822
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0222590
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.6241.9673518
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8885328
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.92121.963107
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.31515404
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.3851526
X-RAY DIFFRACTIONr_chiral_restr0.1080.2404
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.021958
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2380.21406
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3050.21786
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1570.2267
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1740.251
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2360.222
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.0081.51678
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.62122634
X-RAY DIFFRACTIONr_scbond_it2.49431022
X-RAY DIFFRACTIONr_scangle_it4.0664.5884
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.85→1.898 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.339 116 -
Rwork0.259 2324 -
obs--92.18 %

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