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- PDB-8p7s: The impact of molecular variants, crystallization conditions and ... -

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Basic information

Entry
Database: PDB / ID: 8p7s
TitleThe impact of molecular variants, crystallization conditions and space group on structure-ligand complexes: A case study on Bacterial Phosphotriesterase Variants and complexes
ComponentsParathion hydrolase
KeywordsHYDROLASE
Function / homology
Function and homology information


aryldialkylphosphatase activity / aryldialkylphosphatase / 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 hydrolase / Twin arginine translocation (Tat) signal profile. / Twin-arginine translocation pathway, signal sequence
Similarity search - Domain/homology
1-ethyl-1-methyl-cyclohexane / FORMIC ACID / O-ETHYLMETHYLPHOSPHONIC ACID ESTER GROUP / Parathion hydrolase
Similarity search - Component
Biological speciesBrevundimonas diminuta (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.77 Å
AuthorsDym, O. / Aggarwal, N. / Ashani, Y. / Albeck, S. / Unger, T. / Hamer Rogotner, S. / Silman, I. / Sussman, J.L.
Funding support Israel, 1items
OrganizationGrant numberCountry
Israel Science Foundation Israel
CitationJournal: Acta Crystallogr D Struct Biol / Year: 2023
Title: The impact of molecular variants, crystallization conditions and the space group on ligand-protein complexes: a case study on bacterial phosphotriesterase.
Authors: Dym, O. / Aggarwal, N. / Ashani, Y. / Leader, H. / Albeck, S. / Unger, T. / Hamer-Rogotner, S. / Silman, I. / Tawfik, D.S. / Sussman, J.L.
History
DepositionMay 31, 2023Deposition site: PDBE / Processing site: PDBE
SupersessionOct 25, 2023ID: 6FW1
Revision 1.0Oct 25, 2023Provider: repository / Type: Initial release
Revision 1.1Nov 1, 2023Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Nov 8, 2023Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID

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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)36,0599
Polymers35,3781
Non-polymers6818
Water6,143341
1
A: Parathion hydrolase
hetero molecules

A: Parathion hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,11918
Polymers70,7562
Non-polymers1,36316
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Buried area5410 Å2
ΔGint-194 kcal/mol
Surface area22520 Å2
MethodPISA
Unit cell
Length a, b, c (Å)69.540, 69.540, 185.840
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-742-

HOH

21A-770-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Parathion hydrolase / Phosphotriesterase / PTE


Mass: 35378.098 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 , 7 types, 349 molecules

#2: Chemical ChemComp-FMT / FORMIC ACID


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


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-E8N / 1-ethyl-1-methyl-cyclohexane


Mass: 126.239 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H18 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4 / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2 / Feature type: SUBJECT OF INVESTIGATION
#7: Chemical ChemComp-VX / O-ETHYLMETHYLPHOSPHONIC ACID ESTER GROUP


Mass: 124.076 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H9O3P / Feature type: SUBJECT OF INVESTIGATION
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 341 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 3.18 Å3/Da / Density % sol: 61.26 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 1.0M (NH4)2SO4 12% Glycerol 0.1M Tris pH=7.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH3R / Wavelength: 1.541 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: May 22, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.541 Å / Relative weight: 1
ReflectionResolution: 1.77→33.77 Å / Num. obs: 45145 / % possible obs: 99.89 % / Redundancy: 11.8 % / CC1/2: 0.888 / Rpim(I) all: 0.09951 / Net I/σ(I): 30.97
Reflection shellResolution: 1.77→1.84 Å / Mean I/σ(I) obs: 12.07 / Num. unique obs: 4428 / CC1/2: 0.914 / Rpim(I) all: 0.121

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Processing

Software
NameVersionClassification
PHENIX(1.15.2_3472: ???)refinement
HKL-3000data reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.77→33.77 Å / SU ML: 0.15 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 15.67 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.182 2274 5.04 %
Rwork0.158 --
obs0.159 45114 99.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.77→33.77 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2466 0 35 341 2842
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0062642
X-RAY DIFFRACTIONf_angle_d0.9233591
X-RAY DIFFRACTIONf_dihedral_angle_d3.4472108
X-RAY DIFFRACTIONf_chiral_restr0.054415
X-RAY DIFFRACTIONf_plane_restr0.005463
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.774-1.81250.21791450.20912612X-RAY DIFFRACTION100
1.8125-1.85470.20971460.17332609X-RAY DIFFRACTION100
1.8547-1.90110.19741330.15752625X-RAY DIFFRACTION100
1.9011-1.95250.16111310.14872648X-RAY DIFFRACTION100
1.9525-2.00990.16861190.15032647X-RAY DIFFRACTION100
2.0099-2.07480.1771380.15472653X-RAY DIFFRACTION100
2.0748-2.14890.19421470.15632632X-RAY DIFFRACTION100
2.1489-2.2350.19411590.15182641X-RAY DIFFRACTION100
2.235-2.33660.15881590.15172631X-RAY DIFFRACTION100
2.3366-2.45980.19171260.15772674X-RAY DIFFRACTION100
2.4598-2.61390.1971420.162661X-RAY DIFFRACTION100
2.6139-2.81560.19421630.16592670X-RAY DIFFRACTION100
2.8156-3.09880.2171260.16962721X-RAY DIFFRACTION100
3.0988-3.54670.17391540.16532702X-RAY DIFFRACTION100
3.5467-4.46690.14651430.13732774X-RAY DIFFRACTION100
4.4669-100.18461430.15992940X-RAY DIFFRACTION100

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