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Basic information

Entry
Database: PDB / ID: 6gbj
TitleRepertoires of functionally diverse enzymes through computational design at epistatic active-site positions
ComponentsParathion hydrolase
KeywordsHYDROLASE / Phosphotriesterase
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 / Parathion hydrolase
Similarity search - Component
Biological speciesBrevundimonas diminuta (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.63 Å
AuthorsKhersonsky, O. / Lipsh, R. / Avizemer, Z. / Goldsmith, M. / Ashani, Y. / Leader, H. / Dym, O. / Rogotner, S. / Trudeau, D. / Tawfik, D.S. / Fleishman, S.J.
CitationJournal: Mol. Cell / Year: 2018
Title: Automated Design of Efficient and Functionally Diverse Enzyme Repertoires.
Authors: Khersonsky, O. / Lipsh, R. / Avizemer, Z. / Ashani, Y. / Goldsmith, M. / Leader, H. / Dym, O. / Rogotner, S. / Trudeau, D.L. / Prilusky, J. / Amengual-Rigo, P. / Guallar, V. / Tawfik, D.S. / Fleishman, S.J.
History
DepositionApr 15, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 24, 2018Provider: 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 / pdbx_struct_conn_angle / struct_conn / struct_conn_type
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_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_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,67715
Polymers36,7151
Non-polymers96214
Water4,089227
1
A: Parathion hydrolase
hetero molecules

A: Parathion hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,35430
Polymers73,4312
Non-polymers1,92328
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_665-y+1,-x+1,-z+1/21
Buried area7980 Å2
ΔGint-168 kcal/mol
Surface area22760 Å2
MethodPISA
Unit cell
Length a, b, c (Å)69.490, 69.490, 186.020
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
Components on special symmetry positions
IDModelComponents
11A-708-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Parathion hydrolase / Phosphotriesterase / PTE


Mass: 36715.418 Da / Num. of mol.: 1
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 , 5 types, 241 molecules

#2: Chemical ChemComp-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CH2O2
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Formula: SO4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 227 / 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: 3.06 Å3/Da / Density % sol: 59.78 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: 0.1M HEPES pH=7 1.7M Li2SO4

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH3R / Wavelength: 1.5419 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Nov 6, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5419 Å / Relative weight: 1
ReflectionResolution: 1.63→38.65 Å / Num. obs: 57720 / % possible obs: 99.7 % / Redundancy: 5.3 % / Biso Wilson estimate: 16.55 Å2 / Rsym value: 0.04777 / Net I/σ(I): 13.53
Reflection shellResolution: 1.63→1.688 Å / Redundancy: 5.1 % / Mean I/σ(I) obs: 2.81 / Num. unique obs: 5611 / Rsym value: 0.3708 / % possible all: 98.79

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Processing

Software
NameVersionClassification
REFMAC5.8.0222refinement
MOSFLMdata reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1HYZ

1hyz


Resolution: 1.63→38.65 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.959 / SU B: 1.257 / SU ML: 0.043 / Cross valid method: THROUGHOUT / ESU R: 0.069 / ESU R Free: 0.068 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.18127 2889 5 %RANDOM
Rwork0.16258 ---
obs0.16352 54923 99.68 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 17.292 Å2
Baniso -1Baniso -2Baniso -3
1-0.28 Å20 Å2-0 Å2
2--0.28 Å2-0 Å2
3----0.55 Å2
Refinement stepCycle: 1 / Resolution: 1.63→38.65 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2546 0 52 227 2825
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0152649
X-RAY DIFFRACTIONr_bond_other_d0.0010.0172380
X-RAY DIFFRACTIONr_angle_refined_deg1.9631.7553584
X-RAY DIFFRACTIONr_angle_other_deg0.6511.7195557
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3955333
X-RAY DIFFRACTIONr_dihedral_angle_2_deg27.66816.18697
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.27915356
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.9771527
X-RAY DIFFRACTIONr_chiral_restr0.0950.2357
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.0213003
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02481
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_it1.4341.5711329
X-RAY DIFFRACTIONr_mcbond_other1.4341.5711330
X-RAY DIFFRACTIONr_mcangle_it1.9292.351663
X-RAY DIFFRACTIONr_mcangle_other1.9312.351664
X-RAY DIFFRACTIONr_scbond_it2.9021.8851320
X-RAY DIFFRACTIONr_scbond_other2.8071.8481308
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.0352.6631904
X-RAY DIFFRACTIONr_long_range_B_refined4.33420.5722949
X-RAY DIFFRACTIONr_long_range_B_other4.21820.3422915
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.629→1.671 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.24 199 -
Rwork0.23 3955 -
obs--98.39 %

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