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- PDB-3wml: Structure of phosphotriesterase mutant (S308L/Y309A) from Agrobac... -

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Basic information

Entry
Database: PDB / ID: 3wml
TitleStructure of phosphotriesterase mutant (S308L/Y309A) from Agrobacterium radiobacter
ComponentsPhosphotriesterase
KeywordsHYDROLASE / Phosphotriesterase
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
: / : / Phosphotriesterase
Similarity search - Component
Biological speciesAgrobacterium tumefaciens (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.99 Å
AuthorsJackson, C.J. / Carr, P.D. / Sugrue, E.
CitationJournal: Plos One / Year: 2014
Title: A 5000-fold increase in the specificity of a bacterial phosphotriesterase for malathion through combinatorial active site mutagenesis
Authors: Naqvi, T. / Warden, A.C. / French, N. / Sugrue, E. / Carr, P.D. / Jackson, C.J. / Scott, C.
History
DepositionNov 21, 2013Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 24, 2014Provider: repository / Type: Initial release
Revision 1.1Feb 4, 2015Group: Other
Revision 1.2Nov 20, 2019Group: Database references / Derived calculations
Category: pdbx_struct_conn_angle / struct_conn ...pdbx_struct_conn_angle / struct_conn / struct_conn_type / struct_ref_seq_dif
Item: _struct_conn_type.id / _struct_ref_seq_dif.details
Revision 1.3Nov 8, 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_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_comp_id / _struct_conn.ptnr1_auth_seq_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_conn.ptnr2_label_seq_id / _struct_conn_type.id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Dec 6, 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)35,7854
Polymers35,6091
Non-polymers1773
Water2,792155
1
A: Phosphotriesterase
hetero molecules

A: Phosphotriesterase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,5718
Polymers71,2172
Non-polymers3546
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555y,x,-z1
Buried area3830 Å2
ΔGint-57 kcal/mol
Surface area23040 Å2
MethodPISA
Unit cell
Length a, b, c (Å)108.996, 108.996, 61.774
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: 35608.598 Da / Num. of mol.: 1 / Fragment: UNP residues 32-360 / Mutation: S308L, Y309A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Agrobacterium tumefaciens (bacteria) / Gene: opdA / Plasmid: PETMCS1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: Q93LD7, aryldialkylphosphatase
#2: Chemical ChemComp-FE2 / FE (II) ION


Mass: 55.845 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe
#3: Chemical ChemComp-CO / COBALT (II) ION


Mass: 58.933 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Co
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 155 / 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: 2.97 Å3/Da / Density % sol: 58.65 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 20% PEG3350, 0.2M NANO3, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SEALED TUBE / Type: OTHER / Wavelength: 1.5418 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Feb 22, 2013 / Details: Mirrors
RadiationMonochromator: Mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.987→29.355 Å / Num. all: 29386 / Num. obs: 29366 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 10.8 % / Rmerge(I) obs: 0.122 / Net I/σ(I): 20.2
Reflection shellResolution: 1.99→2.04 Å / Redundancy: 9.9 % / Rmerge(I) obs: 0.75 / Mean I/σ(I) obs: 4 / Num. unique all: 29386 / % possible all: 99.8

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Processing

Software
NameVersionClassification
MAR345dtbdata collection
MOLREPphasing
REFMAC5.7.0032refinement
XDSdata reduction
Aimlessdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2D2J

2d2j


Resolution: 1.99→29.355 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.946 / SU B: 2.494 / SU ML: 0.07 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.125 / ESU R Free: 0.117 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.18672 1494 5.1 %RANDOM
Rwork0.15668 ---
all0.1582 27872 --
obs0.1582 27872 99.82 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 19.483 Å2
Baniso -1Baniso -2Baniso -3
1--0.09 Å2-0.09 Å2-0 Å2
2---0.09 Å2-0 Å2
3---0.29 Å2
Refinement stepCycle: LAST / Resolution: 1.99→29.355 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2506 0 6 155 2667
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0220.0192560
X-RAY DIFFRACTIONr_bond_other_d0.0010.022482
X-RAY DIFFRACTIONr_angle_refined_deg2.0841.9633475
X-RAY DIFFRACTIONr_angle_other_deg1.30935683
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4785328
X-RAY DIFFRACTIONr_dihedral_angle_2_deg28.96522.075106
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.42315407
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.9241526
X-RAY DIFFRACTIONr_chiral_restr0.1320.2402
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.0212895
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02593
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.7551.7561315
X-RAY DIFFRACTIONr_mcbond_other1.7531.7541314
X-RAY DIFFRACTIONr_mcangle_it2.3782.6181642
X-RAY DIFFRACTIONr_mcangle_other2.3782.621643
X-RAY DIFFRACTIONr_scbond_it2.7862.0341245
X-RAY DIFFRACTIONr_scbond_other2.7842.0341245
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.1882.9351834
X-RAY DIFFRACTIONr_long_range_B_refined5.15214.6363026
X-RAY DIFFRACTIONr_long_range_B_other5.11214.5372979
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.987→2.038 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.278 96 -
Rwork0.212 1969 -
obs--98.1 %

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