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- PDB-8p7u: The impact of molecular variants, crystallization conditions and ... -

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Basic information

Entry
Database: PDB / ID: 8p7u
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 / cyclohexa-2,5-diene-1,1-diol / Parathion hydrolase
Similarity search - Component
Biological speciesBrevundimonas diminuta (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.38 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: 6G23
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

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Assembly

Deposited unit
A: Parathion hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,4439
Polymers35,7481
Non-polymers6958
Water6,521362
1
A: Parathion hydrolase
hetero molecules

A: Parathion hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,88618
Polymers71,4952
Non-polymers1,39116
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Buried area4370 Å2
ΔGint-24 kcal/mol
Surface area22410 Å2
MethodPISA
Unit cell
Length a, b, c (Å)69.690, 69.690, 187.070
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Parathion hydrolase / Phosphotriesterase / PTE


Mass: 35747.582 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, 370 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-X3T / cyclohexa-2,5-diene-1,1-diol


Mass: 112.127 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H8O2 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3 / Feature type: SUBJECT OF INVESTIGATION
#6: 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
#7: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4 / Feature type: SUBJECT OF INVESTIGATION
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 362 / 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: 61.28 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8 / Details: 1.5M (NH4)2SO4 12% Glycerol 0.1M Tris pH=8.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 1.27242 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jan 7, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.27242 Å / Relative weight: 1
ReflectionResolution: 1.376→18.12 Å / Num. obs: 96151 / % possible obs: 99.15 % / Redundancy: 6.5 % / CC1/2: 0.992 / Rpim(I) all: 0.05118 / Net I/σ(I): 6.87
Reflection shellResolution: 1.38→1.42 Å / Num. unique obs: 9438 / CC1/2: 0.776 / Rpim(I) all: 0.274 / % possible all: 98.7

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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: 1.38→18.12 Å / SU ML: 0.14 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 16.78 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.18 4684 4.9 %
Rwork0.171 --
obs0.171 95540 99.2 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.38→18.12 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2481 0 39 362 2882
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0062597
X-RAY DIFFRACTIONf_angle_d1.0183534
X-RAY DIFFRACTIONf_dihedral_angle_d9.8411477
X-RAY DIFFRACTIONf_chiral_restr0.081418
X-RAY DIFFRACTIONf_plane_restr0.006453
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.38-1.39160.29361560.26882976X-RAY DIFFRACTION99
1.3916-1.4080.24861410.24862960X-RAY DIFFRACTION99
1.408-1.42520.29131600.23092946X-RAY DIFFRACTION99
1.4252-1.44320.24771590.22122965X-RAY DIFFRACTION99
1.4432-1.46220.22911440.20892962X-RAY DIFFRACTION99
1.4622-1.48220.21731640.20583000X-RAY DIFFRACTION99
1.4822-1.50340.22241760.20442944X-RAY DIFFRACTION99
1.5034-1.52580.20451540.19332965X-RAY DIFFRACTION99
1.5258-1.54960.19161580.18353005X-RAY DIFFRACTION99
1.5496-1.5750.211370.17873006X-RAY DIFFRACTION99
1.575-1.60220.20361550.18582982X-RAY DIFFRACTION99
1.6022-1.63130.18421510.18172999X-RAY DIFFRACTION99
1.6313-1.66260.20031530.18013018X-RAY DIFFRACTION99
1.6626-1.69650.19791400.18623002X-RAY DIFFRACTION99
1.6965-1.73340.19561510.1733002X-RAY DIFFRACTION99
1.7334-1.77370.17991720.17262986X-RAY DIFFRACTION99
1.7737-1.8180.19591610.16413002X-RAY DIFFRACTION99
1.818-1.86710.18191550.16753020X-RAY DIFFRACTION99
1.8671-1.9220.16821630.16723030X-RAY DIFFRACTION99
1.922-1.9840.17531510.16893015X-RAY DIFFRACTION99
1.984-2.05480.16231660.16233026X-RAY DIFFRACTION99
2.0548-2.13690.14841350.1483054X-RAY DIFFRACTION99
2.1369-2.2340.18921650.16133040X-RAY DIFFRACTION100
2.234-2.35160.16231480.16233065X-RAY DIFFRACTION100
2.3516-2.49850.17761660.17083051X-RAY DIFFRACTION100
2.4985-2.69090.19521560.17333086X-RAY DIFFRACTION99
2.6909-2.96060.18771660.17953081X-RAY DIFFRACTION100
2.9606-3.38660.18051580.17373147X-RAY DIFFRACTION100
3.3866-4.25760.16291480.14693195X-RAY DIFFRACTION100
4.2576-100.14931750.14933326X-RAY DIFFRACTION99

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