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- PDB-3uf9: Crystal structure of SsoPox in complex with the phosphotriester f... -

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Basic information

Entry
Database: PDB / ID: 3uf9
TitleCrystal structure of SsoPox in complex with the phosphotriester fensulfothion
ComponentsAryldialkylphosphatase
KeywordsHYDROLASE / (Beta/alpha)8-hydrolase / Lactonase
Function / homology
Function and homology information


aryldialkylphosphatase / aryldialkylphosphatase activity / 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
: / : / Chem-FST / Aryldialkylphosphatase
Similarity search - Component
Biological speciesSulfolobus solfataricus (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.68 Å
AuthorsElias, M. / Gotthard, G. / Hiblot, J. / Chabriere, E.
CitationJournal: Sci Rep / Year: 2012
Title: Characterisation of the organophosphate hydrolase catalytic activity of SsoPox
Authors: Hiblot, J. / Gotthard, G. / Chabriere, E. / Elias, M.
History
DepositionOct 31, 2011Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Oct 3, 2012Provider: repository / Type: Initial release
Revision 1.1Oct 10, 2012Group: Structure summary
Revision 1.2May 22, 2013Group: Database references
Revision 1.3Nov 6, 2013Group: Data collection
Revision 1.4Nov 1, 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_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_asym_id / _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.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_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.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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Dec 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

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)144,60019
Polymers142,6324
Non-polymers1,96915
Water2,792155
1
A: Aryldialkylphosphatase
C: Aryldialkylphosphatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,34610
Polymers71,3162
Non-polymers1,0308
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4370 Å2
ΔGint-47 kcal/mol
Surface area22890 Å2
MethodPISA
2
B: Aryldialkylphosphatase
D: Aryldialkylphosphatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,2549
Polymers71,3162
Non-polymers9387
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4180 Å2
ΔGint-48 kcal/mol
Surface area22910 Å2
MethodPISA
Unit cell
Length a, b, c (Å)85.730, 103.760, 151.760
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: 35657.906 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sulfolobus solfataricus (archaea) / Gene: php, SSO2522 / Production host: Escherichia coli (E. coli) / References: UniProt: Q97VT7, aryldialkylphosphatase

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Non-polymers , 5 types, 170 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-FST / O,O-diethyl O-{4-[(R)-methylsulfinyl]phenyl} phosphorothioate / Fensulfothion


Mass: 308.354 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C11H17O4PS2
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#6: 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: 2.37 Å3/Da / Density % sol: 48.02 %
Crystal growTemperature: 277 K / Method: vapor diffusion / pH: 8
Details: 50mM TRIS-HCL PH 8, 23-25% PEG 8000, VAPOR DIFFUSION, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: May 14, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.68→45.4705 Å / Num. obs: 38674

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Processing

Software
NameVersionClassification
MOLREPphasing
REFMAC5.6.0117refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2VC5

2vc5


Resolution: 2.68→45.47 Å / Cor.coef. Fo:Fc: 0.89 / Cor.coef. Fo:Fc free: 0.863 / SU B: 31.31 / SU ML: 0.309 / Cross valid method: THROUGHOUT / ESU R Free: 0.402 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.27541 1934 5 %RANDOM
Rwork0.23945 ---
obs0.24121 36740 99.83 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 34.479 Å2
Baniso -1Baniso -2Baniso -3
1-0.33 Å20 Å20 Å2
2--0.18 Å20 Å2
3----0.51 Å2
Refinement stepCycle: LAST / Resolution: 2.68→45.47 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10052 0 98 155 10305
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0030.0210601
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg0.7311.97414309
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.68751295
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.82924.35492
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.565151911
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.1381567
X-RAY DIFFRACTIONr_chiral_restr0.0540.21586
X-RAY DIFFRACTIONr_gen_planes_refined0.0020.0217971
X-RAY DIFFRACTIONr_gen_planes_other
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_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.68→2.749 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.398 130 -
Rwork0.368 2473 -
obs--100 %
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)
10.3168-0.1398-0.05020.6983-0.13791.17760.0530.00410.0105-0.0652-0.05240.02230.0579-0.0139-0.00060.02280.0002-0.00090.08460.00020.107-23.434613.6447-26.3864
20.46790.18250.07190.3911-0.20121.49430.0071-0.00780.03520.02480.0137-0.03550.0163-0.0346-0.02080.00710.01670.01160.08350.01610.1169-66.36210.89-91.496
30.1524-0.0895-0.02550.6073-0.02511.63170.00710.0116-0.0373-0.0168-0.0586-0.0579-0.12580.07760.05160.06590.010.01270.05920.02320.1005-15.8215.79811.928
40.3626-0.03350.12250.0941-0.18431.89550.0008-0.0289-0.03140.04110.008-0.0207-0.2222-0.0313-0.00880.0925-0.0026-0.01380.04020.00990.0908-65.202917.9928-52.9612
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 314
2X-RAY DIFFRACTION2B1 - 314
3X-RAY DIFFRACTION3C1 - 314
4X-RAY DIFFRACTION4D1 - 314

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