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- PDB-6frz: Phosphotriesterase PTE_A53_7 -

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Basic information

Entry
Database: PDB / ID: 6frz
TitlePhosphotriesterase PTE_A53_7
ComponentsParathion hydrolase
KeywordsHYDROLASE / Metalloenzyme / TIM barrel
Function / homology
Function and homology information


aryldialkylphosphatase / aryldialkylphosphatase activity / catabolic process / zinc ion binding / plasma membrane
Similarity search - Function
Aryldialkylphosphatase, zinc-binding site / Phosphotriesterase family signature 1. / Phosphotriesterase / Phosphotriesterase family / Phosphotriesterase family profile. / Metal-dependent hydrolases / Metal-dependent hydrolase / Twin arginine translocation (Tat) signal profile. / Twin-arginine translocation pathway, signal sequence / TIM Barrel ...Aryldialkylphosphatase, zinc-binding site / Phosphotriesterase family signature 1. / Phosphotriesterase / Phosphotriesterase family / Phosphotriesterase family profile. / Metal-dependent hydrolases / Metal-dependent hydrolase / Twin arginine translocation (Tat) signal profile. / Twin-arginine translocation pathway, signal sequence / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
5-methylcyclohexane-1,1,3,3-tetrol / FORMIC ACID / DI(HYDROXYETHYL)ETHER / TRIETHYLENE GLYCOL / Parathion hydrolase
Similarity search - Component
Biological speciesBrevundimonas diminuta (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.65 Å
AuthorsDym, O. / Aggarwal, N. / Albeck, S. / Unger, T. / Hamer Rogotner, S. / Silman, I. / Leader, H. / Ashani, Y. / Goldsmith, M. / Greisen, P. ...Dym, O. / Aggarwal, N. / Albeck, S. / Unger, T. / Hamer Rogotner, S. / Silman, I. / Leader, H. / Ashani, Y. / Goldsmith, M. / Greisen, P. / Tawfik, D. / Sussman, L.J.
Funding support United States, 2items
OrganizationGrant numberCountry
DTRAHDTRA1-11-C-0026). United States
DTRACB10265 / HDTRA1724528 United States
CitationJournal: To Be Published
Title: Phosphotriesterase PTE_A53_7
Authors: Dym, O. / Aggarwal, N. / Albeck, S. / Unger, T. / Hamer Rogotner, S. / Silman, I. / Leader, H. / Ashani, Y. / Goldsmith, M. / Greisen, P. / Tawfik, D. / Sussman, L.J.
History
DepositionFeb 18, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 13, 2019Provider: repository / Type: Initial release
Revision 1.1Jan 17, 2024Group: 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 / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Parathion hydrolase
B: Parathion hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,69013
Polymers73,5132
Non-polymers1,17711
Water6,954386
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4610 Å2
ΔGint-98 kcal/mol
Surface area23560 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.350, 81.125, 70.583
Angle α, β, γ (deg.)90.00, 94.94, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Parathion hydrolase / Phosphotriesterase / PTE


Mass: 36756.648 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Brevundimonas diminuta (bacteria) / Gene: opd / Production host: Escherichia coli (E. coli) / References: UniProt: P0A434, aryldialkylphosphatase

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Non-polymers , 8 types, 397 molecules

#2: Chemical ChemComp-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: CH2O2
#3: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#4: Chemical ChemComp-E4T / 5-methylcyclohexane-1,1,3,3-tetrol


Mass: 162.184 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H14O4
#5: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#6: Chemical ChemComp-P6G / HEXAETHYLENE GLYCOL / POLYETHYLENE GLYCOL PEG400


Mass: 282.331 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H26O7 / Comment: precipitant*YM
#7: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#8: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 386 / 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: 2.11 Å3/Da / Density % sol: 41.67 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 10% PEG 8000 0.05M Tris pH=7.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH3R / Wavelength: 1.5415 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Apr 28, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5415 Å / Relative weight: 1
ReflectionResolution: 1.65→24.19 Å / Num. obs: 73193 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.4 % / Rsym value: 0.066 / Net I/σ(I): 15.19
Reflection shellResolution: 1.65→1.71 Å / Redundancy: 4.3 % / Mean I/σ(I) obs: 5.3 / Num. unique obs: 7292 / Rsym value: 0.261 / % possible all: 99.6

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Processing

Software
NameVersionClassification
PHENIX(1.11.1-2575_1692: ???)refinement
HKL-3000data reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1HZY

1hzy


Resolution: 1.65→24.193 Å / SU ML: 0.15 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 17.65 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1805 3690 5.04 %
Rwork0.161 --
obs0.162 73186 99.78 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.65→24.193 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5022 0 65 386 5473
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0065186
X-RAY DIFFRACTIONf_angle_d0.9417037
X-RAY DIFFRACTIONf_dihedral_angle_d6.954211
X-RAY DIFFRACTIONf_chiral_restr0.053823
X-RAY DIFFRACTIONf_plane_restr0.006906
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6501-1.67180.20511290.16642639X-RAY DIFFRACTION99
1.6718-1.69470.2091220.16962692X-RAY DIFFRACTION100
1.6947-1.71890.20691430.15892660X-RAY DIFFRACTION100
1.7189-1.74460.2241510.18172684X-RAY DIFFRACTION100
1.7446-1.77180.23221250.18932670X-RAY DIFFRACTION100
1.7718-1.80090.21151410.17552672X-RAY DIFFRACTION100
1.8009-1.83190.20491350.16292639X-RAY DIFFRACTION100
1.8319-1.86520.18321380.16582718X-RAY DIFFRACTION100
1.8652-1.90110.1691600.15752624X-RAY DIFFRACTION100
1.9011-1.93990.19161280.15832713X-RAY DIFFRACTION100
1.9399-1.9820.18561600.15932619X-RAY DIFFRACTION100
1.982-2.02810.19891310.16792713X-RAY DIFFRACTION100
2.0281-2.07880.21341450.17052664X-RAY DIFFRACTION100
2.0788-2.1350.19441300.16062665X-RAY DIFFRACTION100
2.135-2.19780.19461460.1592677X-RAY DIFFRACTION100
2.1978-2.26860.16431550.15032664X-RAY DIFFRACTION100
2.2686-2.34970.1941570.15982639X-RAY DIFFRACTION100
2.3497-2.44370.16441470.16332696X-RAY DIFFRACTION100
2.4437-2.55480.19591560.16392635X-RAY DIFFRACTION100
2.5548-2.68930.17291240.16442662X-RAY DIFFRACTION99
2.6893-2.85750.17711540.16822683X-RAY DIFFRACTION100
2.8575-3.07780.20271230.17162691X-RAY DIFFRACTION99
3.0778-3.38670.20011560.17892669X-RAY DIFFRACTION99
3.3867-3.87510.1561390.15542687X-RAY DIFFRACTION100
3.8751-4.87560.15061430.13682690X-RAY DIFFRACTION100
4.8756-24.19520.16341520.15642731X-RAY DIFFRACTION100

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