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- PDB-8p7f: The impact of molecular variants, crystallization conditions and ... -

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Basic information

Entry
Database: PDB / ID: 8p7f
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 / 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 hydrolase / Twin arginine translocation (Tat) signal profile. / Twin-arginine translocation pathway, signal sequence
Similarity search - Domain/homology
Biological speciesBrevundimonas diminuta (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 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 30, 2023Deposition site: PDBE / Processing site: PDBE
SupersessionNov 1, 2023ID: 6FEE
Revision 1.0Nov 1, 2023Provider: repository / Type: Initial release
Revision 1.1Nov 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)35,9302
Polymers35,8651
Non-polymers651
Water1,51384
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area100 Å2
ΔGint-39 kcal/mol
Surface area12180 Å2
Unit cell
Length a, b, c (Å)79.700, 93.670, 44.590
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein Parathion hydrolase / Phosphotriesterase / PTE


Mass: 35864.684 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
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 84 / Source method: isolated from a natural source / Formula: H2O
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: 2.32 Å3/Da / Density % sol: 46.99 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 12% PEG 6,000 5% MPD 0.1M HEPES pH=7.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.9763 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Nov 25, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 2→40.261 Å / Num. obs: 23037 / % possible obs: 98.91 % / Redundancy: 5.3 % / CC1/2: 0.75 / Net I/σ(I): 12.5
Reflection shellResolution: 2→2.071 Å / Num. unique obs: 2273 / CC1/2: 0.638

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Processing

Software
NameVersionClassification
PHENIX(1.15.2_3472: ???)refinement
HKL-2000data reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→40.261 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 25.02 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2398 1187 5.16 %
Rwork0.2044 --
obs0.2062 23011 98.93 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2→40.261 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2150 0 1 84 2235
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072196
X-RAY DIFFRACTIONf_angle_d0.7962983
X-RAY DIFFRACTIONf_dihedral_angle_d2.4541773
X-RAY DIFFRACTIONf_chiral_restr0.051360
X-RAY DIFFRACTIONf_plane_restr0.006378
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.0910.27511280.23982709X-RAY DIFFRACTION100
2.091-2.20130.27191490.22862694X-RAY DIFFRACTION100
2.2013-2.33920.27761380.21652747X-RAY DIFFRACTION100
2.3392-2.51980.22981500.21942693X-RAY DIFFRACTION100
2.5198-2.77330.24191660.21682735X-RAY DIFFRACTION100
2.7733-3.17440.25851680.20912728X-RAY DIFFRACTION100
3.1744-3.99890.20341640.19912780X-RAY DIFFRACTION100
3.9989-4.20.24721240.18772738X-RAY DIFFRACTION93

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