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- PDB-5w3z: Crystal structure of SsoPox AsC6 mutant (L72I-Y99F-I122L-L228M-F2... -

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Basic information

Entry
Database: PDB / ID: 5w3z
TitleCrystal structure of SsoPox AsC6 mutant (L72I-Y99F-I122L-L228M-F229S-W263L)
ComponentsAryldialkylphosphatase
KeywordsHYDROLASE / lactonase / phosphotriesterase / mutants / quorum sensing / organophosphate / organophosphorous / insecticides.
Function / homology
Function and homology information


aryldialkylphosphatase activity / aryldialkylphosphatase / 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 / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
: / : / Aryldialkylphosphatase
Similarity search - Component
Biological speciesSulfolobus solfataricus (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.55 Å
AuthorsHiblot, J. / Gotthard, G. / Jacquet, P. / Daude, D. / Bergonzi, C. / Chabriere, E. / Elias, M.
CitationJournal: Sci Rep / Year: 2017
Title: Rational engineering of a native hyperthermostable lactonase into a broad spectrum phosphotriesterase.
Authors: Jacquet, P. / Hiblot, J. / Daude, D. / Bergonzi, C. / Gotthard, G. / Armstrong, N. / Chabriere, E. / Elias, M.
History
DepositionJun 8, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 10, 2018Provider: repository / Type: Initial release
Revision 1.1Nov 20, 2019Group: Derived calculations / Category: pdbx_struct_conn_angle / struct_conn
Revision 2.0Aug 18, 2021Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Non-polymer description / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / database_2 / entity / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_conn_angle / pdbx_validate_close_contact / struct_conn / struct_conn_type / struct_site / struct_site_gen
Item: _atom_site.auth_comp_id / _atom_site.label_comp_id ..._atom_site.auth_comp_id / _atom_site.label_comp_id / _chem_comp.formula / _chem_comp.id / _chem_comp.name / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity.pdbx_description / _pdbx_entity_nonpoly.comp_id / _pdbx_entity_nonpoly.name / _pdbx_nonpoly_scheme.mon_id / _pdbx_nonpoly_scheme.pdb_mon_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_validate_close_contact.auth_comp_id_1 / _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_site.details / _struct_site.pdbx_auth_comp_id / _struct_site_gen.auth_comp_id / _struct_site_gen.label_comp_id
Revision 2.1Oct 4, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 2.2Nov 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: Aryldialkylphosphatase
B: Aryldialkylphosphatase
C: Aryldialkylphosphatase
D: Aryldialkylphosphatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)143,30722
Polymers142,1074
Non-polymers1,20018
Water2,774154
1
A: Aryldialkylphosphatase
C: Aryldialkylphosphatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,65411
Polymers71,0542
Non-polymers6009
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3890 Å2
ΔGint-63 kcal/mol
Surface area22430 Å2
MethodPISA
2
B: Aryldialkylphosphatase
D: Aryldialkylphosphatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,65411
Polymers71,0542
Non-polymers6009
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4550 Å2
ΔGint-36 kcal/mol
Surface area23590 Å2
MethodPISA
Unit cell
Length a, b, c (Å)81.650, 105.800, 154.530
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 4 molecules ABCD

#1: Protein
Aryldialkylphosphatase / Paraoxonase / SsoPox / Phosphotriesterase-like lactonase


Mass: 35526.797 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sulfolobus solfataricus (archaea) / Production host: Escherichia coli (E. coli) / References: UniProt: Q97VT7, aryldialkylphosphatase

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Non-polymers , 5 types, 172 molecules

#2: Chemical
ChemComp-FE2 / FE (II) ION


Mass: 55.845 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Fe
#3: Chemical
ChemComp-CO / COBALT (II) ION


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


Mass: 62.068 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 154 / 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: 2.35 Å3/Da / Density % sol: 47.74 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 20-30 % (w/v) PEG 8000 and 50 mM Tris-HCl buffer (pH 8)

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 1.00882 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 7, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.00882 Å / Relative weight: 1
ReflectionResolution: 2.55→46.313 Å / Num. obs: 43204 / % possible obs: 97.3 % / Redundancy: 4.49 % / Net I/σ(I): 15.68

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
XDSdata reduction
XSCALEdata scaling
REFMACphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2vc5

2vc5


Resolution: 2.55→46.31 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.928 / SU B: 35.814 / SU ML: 0.32 / Cross valid method: THROUGHOUT / ESU R: 1.157 / ESU R Free: 0.322 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25185 2161 5 %RANDOM
Rwork0.1892 ---
obs0.19237 41042 97.29 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 76.742 Å2
Baniso -1Baniso -2Baniso -3
1-1.01 Å20 Å20 Å2
2--1.85 Å2-0 Å2
3----2.86 Å2
Refinement stepCycle: 1 / Resolution: 2.55→46.31 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9601 0 56 154 9811
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0199849
X-RAY DIFFRACTIONr_bond_other_d0.0050.029444
X-RAY DIFFRACTIONr_angle_refined_deg2.021.96813224
X-RAY DIFFRACTIONr_angle_other_deg1.2321885
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.55451198
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.65724.525453
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.439151789
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.5491558
X-RAY DIFFRACTIONr_chiral_restr0.1180.21500
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0210749
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021949
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_it2.8963.8864813
X-RAY DIFFRACTIONr_mcbond_other2.8973.8854812
X-RAY DIFFRACTIONr_mcangle_it4.8045.8146004
X-RAY DIFFRACTIONr_mcangle_other4.8035.8156005
X-RAY DIFFRACTIONr_scbond_it2.884.1565036
X-RAY DIFFRACTIONr_scbond_other2.884.1565037
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.786.1437221
X-RAY DIFFRACTIONr_long_range_B_refined8.08746.49211176
X-RAY DIFFRACTIONr_long_range_B_other8.08646.49211176
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.55→2.616 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.38 159 -
Rwork0.352 3010 -
obs--97.45 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.06410.0150.2940.70970.84274.49690.1329-0.01560.0850.1078-0.0319-0.19050.4356-0.2666-0.1010.4187-0.06240.10060.17990.00560.258-21.6709-9.895918.6402
20.11070.3431-0.59672.2473-0.5984.7202-0.0112-0.0536-0.0412-0.2687-0.1766-0.0547-0.11330.13710.18790.3455-0.0115-0.00150.18220.04070.2209-22.3448-42.120450.3439
30.2447-0.20450.99060.3574-0.78116.65050.14540.08990.1593-0.1382-0.1934-0.05061.1720.21340.04810.48110.0835-0.01510.17350.04350.2886-21.3799-17.9659-21.2832
40.10720.21640.13971.2393-0.18085.62040.00010.1065-0.09990.7212-0.004-0.0174-1.00970.70230.00380.9807-0.302-0.0050.2186-0.09240.2009-16.9547-36.275389.7141
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 314
2X-RAY DIFFRACTION2B1 - 314
3X-RAY DIFFRACTION3C2 - 314
4X-RAY DIFFRACTION4D1 - 314

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