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- PDB-2vc7: Structural basis for natural lactonase and promiscuous phosphotri... -

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Basic information

Entry
Database: PDB / ID: 2vc7
TitleStructural basis for natural lactonase and promiscuous phosphotriesterase activities
ComponentsARYLDIALKYLPHOSPHATASE
KeywordsHYDROLASE / PHOSPHOTRIESTERASE / PROMISCUOUS ACTIVITIES / ENZYME EVOLUTION / HYPERTHERMOPHILIC / LACTONASE / BIOTECHNOLOGY / QUORUM SENSING
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
: / : / Chem-HT5 / Aryldialkylphosphatase
Similarity search - Component
Biological speciesSULFOLOBUS SOLFATARICUS (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.05 Å
AuthorsElias, M. / Dupuy, J. / Merone, L. / Mandrich, L. / Moniot, S. / Rochu, D. / Lecomte, C. / Rossi, M. / Masson, P. / Manco, G. / Chabriere, E.
CitationJournal: J.Mol.Biol. / Year: 2008
Title: Structural Basis for Natural Lactonase and Promiscuous Phosphotriesterase Activities.
Authors: Elias, M. / Dupuy, J. / Merone, L. / Mandrich, L. / Porzio, E. / Moniot, S. / Rochu, D. / Lecomte, C. / Rossi, M. / Masson, P. / Manco, G. / Chabriere, E.
History
DepositionSep 19, 2007Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 15, 2008Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 2.0Jan 22, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Derived calculations / Non-polymer description / Other / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / database_PDB_caveat / entity / pdbx_database_status / pdbx_struct_conn_angle / struct_conn
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _chem_comp.formula / _chem_comp.formula_weight / _entity.formula_weight / _pdbx_database_status.status_code_sf / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr2_label_atom_id
Revision 3.0Aug 18, 2021Group: Atomic model / Data collection ...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 / struct_conn / 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.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_comp_id / _pdbx_struct_conn_angle.ptnr2_label_comp_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.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_site_gen.auth_comp_id / _struct_site_gen.label_comp_id
Revision 3.1Dec 13, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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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)148,30769
Polymers142,6324
Non-polymers5,67565
Water13,691760
1
A: ARYLDIALKYLPHOSPHATASE
B: ARYLDIALKYLPHOSPHATASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,42937
Polymers71,3162
Non-polymers3,11335
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4750 Å2
ΔGint-21 kcal/mol
Surface area27370 Å2
MethodPQS
2
C: ARYLDIALKYLPHOSPHATASE
D: ARYLDIALKYLPHOSPHATASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,87832
Polymers71,3162
Non-polymers2,56230
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4800 Å2
ΔGint-14.6 kcal/mol
Surface area27690 Å2
MethodPQS
Unit cell
Length a, b, c (Å)86.383, 104.124, 153.051
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 / PHOSPHOTRIESTERASE / PARAOXONASE / PHP / SSOPOX


Mass: 35657.906 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 , 6 types, 825 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.: 28 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical...
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 25 / Source method: obtained synthetically / Formula: C2H6O2
#6: Chemical
ChemComp-HT5 / (4S)-4-(decanoylamino)-5-hydroxy-3,4-dihydro-2H-thiophenium


Mass: 271.419 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C14H25NO2S
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 760 / 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: 2.5 Å3/Da / Density % sol: 40.88 % / Description: NONE
Crystal growpH: 8 / Details: TRIS-HCL 50MM PH 8, 15-18% W/V PEG 8000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.934
DetectorType: ADSC CCD / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.934 Å / Relative weight: 1
ReflectionResolution: 2.05→61.66 Å / Num. obs: 141906 / % possible obs: 99.9 % / Observed criterion σ(I): 2 / Redundancy: 7.25 % / Rmerge(I) obs: 0.13 / Net I/σ(I): 13.66
Reflection shellResolution: 2.05→2.15 Å / Redundancy: 7.1 % / % possible all: 92.8

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2VC5

2vc5


Resolution: 2.05→61.66 Å / Cor.coef. Fo:Fc: 0.932 / Cor.coef. Fo:Fc free: 0.896 / SU B: 9.337 / SU ML: 0.232 / Cross valid method: THROUGHOUT / ESU R: 0.282 / ESU R Free: 0.225 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. THE BINDING OF THE LACTONE MIMIC DESCRIBED IN THE ARTICLE IS FROM MONOMER C.
RfactorNum. reflection% reflectionSelection details
Rfree0.287 4370 5 %RANDOM
Rwork0.237 ---
obs0.239 82756 99.9 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 28.86 Å2
Baniso -1Baniso -2Baniso -3
1-0.6 Å20 Å20 Å2
2---0.17 Å20 Å2
3----0.44 Å2
Refinement stepCycle: LAST / Resolution: 2.05→61.66 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10052 0 348 760 11160
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.02211160
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.1191.98315037
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.70851370
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.31524.239519
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.318152008
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.4791577
X-RAY DIFFRACTIONr_chiral_restr0.1040.21632
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.028368
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.180.25635
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.2970.27634
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.0880.2721
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1240.256
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1160.221
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.2571.56868
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.42210850
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it0.28634803
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it0.4384.54185
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.05→2.1 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.369 341
Rwork0.366 6031

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