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- PDB-4kez: Crystal structure of SsoPox W263F -

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Basic information

Entry
Database: PDB / ID: 4kez
TitleCrystal structure of SsoPox W263F
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: 1.85 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

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)144,01024
Polymers142,4754
Non-polymers1,53420
Water18,8981049
1
A: Aryldialkylphosphatase
D: Aryldialkylphosphatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,92811
Polymers71,2382
Non-polymers6909
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5500 Å2
ΔGint-70 kcal/mol
Surface area22870 Å2
MethodPISA
2
B: Aryldialkylphosphatase
C: Aryldialkylphosphatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,08213
Polymers71,2382
Non-polymers84411
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5950 Å2
ΔGint-69 kcal/mol
Surface area22720 Å2
MethodPISA
Unit cell
Length a, b, c (Å)87.130, 103.620, 151.660
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: 35618.867 Da / Num. of mol.: 4 / Mutation: W263F
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 , 5 types, 1069 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-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


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


Mass: 18.015 Da / Num. of mol.: 1049 / 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: 2.4 Å3/Da / Density % sol: 48.81 %
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: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 1.00882 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 7, 2012
RadiationMonochromator: channel cut / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.00882 Å / Relative weight: 1
ReflectionResolution: 1.85→49.03 Å / Num. obs: 117479

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Processing

Software
NameVersionClassificationNB
REFMACrefinement
PDB_EXTRACT3.11data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.85→49.03 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.956 / WRfactor Rfree: 0.1801 / WRfactor Rwork: 0.1451 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.8983 / SU B: 4.791 / SU ML: 0.072 / SU R Cruickshank DPI: 0.1166 / SU Rfree: 0.1111 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.117 / ESU R Free: 0.111 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.1864 5874 5 %RANDOM
Rwork0.1513 ---
obs0.153 117479 99.95 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 106.23 Å2 / Biso mean: 26.8691 Å2 / Biso min: 11.42 Å2
Baniso -1Baniso -2Baniso -3
1-2.69 Å20 Å20 Å2
2---0.56 Å20 Å2
3----2.13 Å2
Refinement stepCycle: LAST / Resolution: 1.85→49.03 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10040 0 78 1049 11167
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0040.0210336
X-RAY DIFFRACTIONr_angle_refined_deg0.8961.97213949
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.18951262
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.58324.419473
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.06151869
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.4581560
X-RAY DIFFRACTIONr_chiral_restr0.0640.21575
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0217696
LS refinement shellResolution: 1.85→1.898 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.225 402 -
Rwork0.189 7756 -
all-8158 -
obs--99.91 %
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)
10.39450.0163-0.15330.57010.02571.25780.0279-0.0313-0.01270.0084-0.06720.0693-0.00880.03220.03930.0033-0.0038-0.00380.0179-0.00630.022724.090613.55126.2762
20.1891-0.06340.14320.57330.08661.3077-0.01390.0163-0.0244-0.0094-0.00180.0453-0.06810.0370.01560.0214-0.01420.02180.0256-0.01880.034667.66510.74591.45
30.147-0.04090.17190.47230.0071.3521-0.0042-0.00720.0216-0.0325-0.018-0.0012-0.03950.02650.02220.00650.00730.00280.0170.00460.019165.677218.118952.8392
40.38370.1571-0.11050.44740.11141.503-0.00160.00380.08460.0395-0.01080.0632-0.0207-0.04630.01230.0306-0.00640.01040.0080.00240.029715.91415.634-12.055
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 314
2X-RAY DIFFRACTION1A401 - 406
3X-RAY DIFFRACTION2B1 - 314
4X-RAY DIFFRACTION2B401 - 405
5X-RAY DIFFRACTION3C1 - 314
6X-RAY DIFFRACTION3C401 - 406
7X-RAY DIFFRACTION4D1 - 314
8X-RAY DIFFRACTION4D401 - 403

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