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- PDB-4kev: Crystal structure of SsoPox W263L -

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Basic information

Entry
Database: PDB / ID: 4kev
TitleCrystal structure of SsoPox W263L
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
: / : / Aryldialkylphosphatase
Similarity search - Component
Biological speciesSulfolobus solfataricus (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.65 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Aryldialkylphosphatase
B: Aryldialkylphosphatase
C: Aryldialkylphosphatase
D: Aryldialkylphosphatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)142,79912
Polymers142,3394
Non-polymers4598
Water3,459192
1
A: Aryldialkylphosphatase
B: Aryldialkylphosphatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,3996
Polymers71,1702
Non-polymers2304
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4070 Å2
ΔGint-72 kcal/mol
Surface area23180 Å2
MethodPISA
2
C: Aryldialkylphosphatase
D: Aryldialkylphosphatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,3996
Polymers71,1702
Non-polymers2304
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3800 Å2
ΔGint-69 kcal/mol
Surface area23560 Å2
MethodPISA
Unit cell
Length a, b, c (Å)83.906, 105.075, 153.888
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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


Mass: 35584.852 Da / Num. of mol.: 4 / Mutation: W263L
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
#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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 192 / 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: 2.38 Å3/Da / Density % sol: 48.38 %
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: Jan 1, 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: 2.65→86.776 Å / Num. obs: 39816

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Processing

Software
NameVersionClassificationNB
REFMACrefinement
PDB_EXTRACT3.11data extraction
MxCuBEdata collection
XDSdata reduction
XDSdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.65→46.14 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.928 / WRfactor Rfree: 0.2383 / WRfactor Rwork: 0.1908 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.8058 / SU B: 31.704 / SU ML: 0.308 / SU R Cruickshank DPI: 0.2732 / SU Rfree: 0.3517 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.353 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.2503 2000 5 %RANDOM
Rwork0.2028 ---
obs0.2053 39816 99.13 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 298.44 Å2 / Biso mean: 79.1204 Å2 / Biso min: 16 Å2
Baniso -1Baniso -2Baniso -3
1-8.3 Å2-0 Å2-0 Å2
2---2.95 Å20 Å2
3----5.35 Å2
Refinement stepCycle: LAST / Resolution: 2.65→46.14 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10028 0 8 192 10228
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0010.01910287
X-RAY DIFFRACTIONr_angle_refined_deg0.4241.96913863
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.03951258
X-RAY DIFFRACTIONr_dihedral_angle_2_deg19.26924.395471
X-RAY DIFFRACTIONr_dihedral_angle_3_deg9.129151869
X-RAY DIFFRACTIONr_dihedral_angle_4_deg9.2061561
X-RAY DIFFRACTIONr_chiral_restr0.0310.21563
X-RAY DIFFRACTIONr_gen_planes_refined0.0010.0217671
X-RAY DIFFRACTIONr_mcbond_it4.5984.5415032
X-RAY DIFFRACTIONr_mcangle_it7.2466.8036287
X-RAY DIFFRACTIONr_scbond_it5.4694.7225255
LS refinement shellResolution: 2.65→2.721 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.403 139 -
Rwork0.322 2605 -
all-2744 -
obs--94.52 %
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)
10.2924-0.1319-0.48021.68550.60576.88950.13090.1032-0.1203-0.09770.0094-0.2176-0.8305-0.267-0.14030.12290.0322-0.03390.16950.03670.2117-22.993411.2651-17.4217
20.37220.2269-0.75890.9718-0.81869.73780.0739-0.118-0.1550.249-0.1226-0.0603-1.72850.20010.04870.3475-0.04330.01170.09620.02890.1534-22.97216.89821.5234
30.7425-1.04861.44344.0172-0.45437.16380.00390.11150.12460.4846-0.3677-0.16810.45210.06050.36390.172-0.01670.03150.06170.05310.1534-23.082841.0391-49.4195
40.5458-0.4629-1.00992.70571.61154.8251-0.1804-0.17420.1387-0.35530.2668-0.34770.48580.4058-0.08640.53930.20790.04350.1553-0.02210.1886-16.623835.9529-88.4075
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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