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- PDB-4ket: Crystal structure of SsoPox W263I -

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Basic information

Entry
Database: PDB / ID: 4ket
TitleCrystal structure of SsoPox W263I
ComponentsAryldialkylphosphatase
KeywordsHYDROLASE / (beta/alpha)8-hydrolase / lactonase
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
: / : / DI(HYDROXYETHYL)ETHER / Aryldialkylphosphatase
Similarity search - Component
Biological speciesSulfolobus solfataricus (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsGotthard, G. / Hiblot, J. / Chabriere, E. / Elias, M.
CitationJournal: Plos One / Year: 2013
Title: Differential Active Site Loop Conformations Mediate Promiscuous Activities in the Lactonase SsoPox.
Authors: Hiblot, J. / Gotthard, G. / Elias, M. / Chabriere, E.
History
DepositionApr 26, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 2, 2013Provider: repository / Type: Initial release
Revision 1.1Nov 20, 2013Group: Database references
Revision 1.2Mar 26, 2025Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / pdbx_struct_conn_angle / 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 / _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_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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)144,74133
Polymers142,3394
Non-polymers2,40129
Water16,214900
1
A: Aryldialkylphosphatase
C: Aryldialkylphosphatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,33216
Polymers71,1702
Non-polymers1,16314
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7160 Å2
ΔGint-54 kcal/mol
Surface area22370 Å2
MethodPISA
2
B: Aryldialkylphosphatase
D: Aryldialkylphosphatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,40817
Polymers71,1702
Non-polymers1,23915
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6570 Å2
ΔGint-57 kcal/mol
Surface area22690 Å2
MethodPISA
Unit cell
Length a, b, c (Å)87.400, 103.900, 150.500
Angle α, β, γ (deg.)90.000, 90.000, 90.000
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: 35584.852 Da / Num. of mol.: 4 / Mutation: W263I
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sulfolobus solfataricus (archaea) / Gene: php, php SSO2522, SSO2522 / Plasmid: pET22b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)-pLysS / References: UniProt: Q97VT7, aryldialkylphosphatase

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Non-polymers , 7 types, 929 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.: 7 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: C3H8O3
#6: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#7: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 900 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY

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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: 2.4 Å3/Da / Density % sol: 48.76 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 50 mM Tris-HCl, 23-25% PEG8000, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.99987 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 11, 2011
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99987 Å / Relative weight: 1
ReflectionResolution: 2→44.66 Å / Num. obs: 92731

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Processing

Software
NameVersionClassificationNB
REFMACrefinement
PDB_EXTRACT3.11data extraction
MxCuBEdata collection
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→44.66 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.945 / WRfactor Rfree: 0.1817 / WRfactor Rwork: 0.1396 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.9037 / SU B: 6.082 / SU ML: 0.085 / SU R Cruickshank DPI: 0.1495 / SU Rfree: 0.1375 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.149 / ESU R Free: 0.137 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.1895 4637 5 %RANDOM
Rwork0.1447 ---
obs0.1469 92730 99.57 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 84.99 Å2 / Biso mean: 24.1689 Å2 / Biso min: 9.54 Å2
Baniso -1Baniso -2Baniso -3
1-1.39 Å20 Å20 Å2
2--0.1 Å20 Å2
3----1.49 Å2
Refinement stepCycle: LAST / Resolution: 2→44.66 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10028 0 135 900 11063
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.0210474
X-RAY DIFFRACTIONr_angle_refined_deg0.9531.97714083
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.25851284
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.30124.376473
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.708151904
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.751563
X-RAY DIFFRACTIONr_chiral_restr0.0640.21592
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0217723
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.229 322 -
Rwork0.168 6113 -
all-6435 -
obs--99.92 %
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)
10.2409-0.05950.09030.53580.02641.1035-0.00150.0263-0.0102-0.0199-0.00370.0393-0.05380.02180.00520.0149-0.00920.01330.0099-0.01060.023567.991-41.26315.432
20.40270.04930.01260.6224-0.06931.30660.0468-0.0326-0.00690.0467-0.06360.04370.03620.02550.01680.0094-0.00710.00220.0088-0.00430.017724.321-38.3574-49.0724
30.25860.00280.13710.42490.02031.2667-0.00470.01190.026-0.0391-0.0101-0.0022-0.05410.02250.01480.01040.0029-0.00090.00280.00170.013165.813-33.6929-22.7818
40.3510.095-0.17370.34970.03741.48030.0081-0.01320.04850.0651-0.01240.0447-0.0714-0.05530.00430.0295-0.00210.00790.0049-0.0020.020215.715-36.18-87.206
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 314
2X-RAY DIFFRACTION1A401 - 407
3X-RAY DIFFRACTION2B1 - 314
4X-RAY DIFFRACTION2B401 - 407
5X-RAY DIFFRACTION3C1 - 314
6X-RAY DIFFRACTION3C401 - 407
7X-RAY DIFFRACTION4D1 - 314
8X-RAY DIFFRACTION4D401 - 408

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