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- PDB-6fu6: Phosphotriesterase PTE_C23_2 -

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Basic information

Entry
Database: PDB / ID: 6fu6
TitlePhosphotriesterase PTE_C23_2
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
FORMIC ACID / POLYACRYLIC ACID / Parathion hydrolase
Similarity search - Component
Biological speciesBrevundimonas diminuta (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.95 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_4
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 26, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 20, 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 / struct_conn_type
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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_type.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)72,61311
Polymers71,6132
Non-polymers1,0009
Water5,224290
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2990 Å2
ΔGint-88 kcal/mol
Surface area22990 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.660, 81.160, 70.660
Angle α, β, γ (deg.)90.00, 94.83, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Parathion hydrolase / Phosphotriesterase / PTE


Mass: 35806.605 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
#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.: 5 / Source method: obtained synthetically / Formula: Zn
#4: Chemical ChemComp-TA8 / POLYACRYLIC ACID / OCTANE-1,3,5,7-TETRACARBOXYLIC ACID


Mass: 290.267 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C12H18O8
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 290 / 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: 2.18 Å3/Da / Density % sol: 43.6 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 0.05M HEPES pH=7.5 13% Polyacrylic acid 5100 Na 0.01M MgCl2

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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: May 25, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5415 Å / Relative weight: 1
ReflectionResolution: 1.95→70.41 Å / Num. obs: 44881 / % possible obs: 99.96 % / Observed criterion σ(F): 0 / Redundancy: 6.1 % / Biso Wilson estimate: 18.32 Å2 / Rmerge(I) obs: 0.05192 / Net I/σ(I): 11.84
Reflection shellResolution: 1.95→2.02 Å / Rmerge(I) obs: 0.248 / Mean I/σ(I) obs: 3.18 / Num. unique obs: 4458 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0189refinement
HKL-3000data reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1HYZ

1hyz


Resolution: 1.95→70.41 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.939 / SU B: 3.461 / SU ML: 0.098 / Cross valid method: THROUGHOUT / ESU R: 0.155 / ESU R Free: 0.139 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19871 2264 5 %RANDOM
Rwork0.15636 ---
obs0.15849 42615 99.98 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 18.565 Å2
Baniso -1Baniso -2Baniso -3
1-0.88 Å2-0 Å20.43 Å2
2--0.18 Å20 Å2
3----1.12 Å2
Refinement stepCycle: 1 / Resolution: 1.95→70.41 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4977 0 31 290 5298
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0195142
X-RAY DIFFRACTIONr_bond_other_d0.0030.024847
X-RAY DIFFRACTIONr_angle_refined_deg1.8651.9636976
X-RAY DIFFRACTIONr_angle_other_deg1.2293.00111158
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.525662
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.20822.617214
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.02615830
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.6071550
X-RAY DIFFRACTIONr_chiral_restr0.110.2813
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0215786
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021088
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.3621.7052642
X-RAY DIFFRACTIONr_mcbond_other1.3621.7052643
X-RAY DIFFRACTIONr_mcangle_it1.9522.5473306
X-RAY DIFFRACTIONr_mcangle_other1.9552.5493307
X-RAY DIFFRACTIONr_scbond_it2.2651.9882500
X-RAY DIFFRACTIONr_scbond_other2.2571.9882498
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.5152.8853670
X-RAY DIFFRACTIONr_long_range_B_refined4.65621.3415891
X-RAY DIFFRACTIONr_long_range_B_other4.62321.2525844
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.95→2.001 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.259 175 -
Rwork0.211 3097 -
obs--100 %

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