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- PDB-8p7i: The impact of molecular variants, crystallization conditions and ... -

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Basic information

Entry
Database: PDB / ID: 8p7i
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
FORMIC ACID / (2~{S},6~{R})-2,6-dimethyl-1,3-dioxane-4,4-diol / Parathion hydrolase
Similarity search - Component
Biological speciesBrevundimonas diminuta (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.7 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
SupersessionOct 25, 2023ID: 6FEI
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
B: Parathion hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,16310
Polymers73,5132
Non-polymers6508
Water9,566531
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3180 Å2
ΔGint-60 kcal/mol
Surface area23530 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.230, 81.249, 70.666
Angle α, β, γ (deg.)90.00, 94.80, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Parathion hydrolase / Phosphotriesterase / PTE


Mass: 36756.648 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.: 4 / Source method: obtained synthetically / Formula: Zn
#4: Chemical ChemComp-X3E / (2~{S},6~{R})-2,6-dimethyl-1,3-dioxane-4,4-diol


Mass: 148.157 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H12O4 / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 531 / 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: 2.14 Å3/Da / Density % sol: 42.51 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 16% PEG 6,000 2% MPD 0.1M HEPES pH=7.5 0.1M Glycine

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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: Jul 1, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.541 Å / Relative weight: 1
ReflectionResolution: 1.699→39.18 Å / Num. obs: 67098 / % possible obs: 99.69 % / Redundancy: 6.1 % / CC1/2: 0.925 / Net I/σ(I): 20.06
Reflection shellResolution: 1.7→1.76 Å / Num. unique obs: 6633 / CC1/2: 0.925

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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: 1.7→39.18 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 18.05 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.181 3397 5.06 %
Rwork0.151 --
obs0.153 67089 99.7 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.7→39.18 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5019 0 30 531 5580
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0065198
X-RAY DIFFRACTIONf_angle_d0.8477074
X-RAY DIFFRACTIONf_dihedral_angle_d3.1994196
X-RAY DIFFRACTIONf_chiral_restr0.051827
X-RAY DIFFRACTIONf_plane_restr0.005918
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7-1.72310.26741470.21492543X-RAY DIFFRACTION97
1.7231-1.74880.22211310.19162695X-RAY DIFFRACTION100
1.7488-1.77620.2181510.17542593X-RAY DIFFRACTION100
1.7762-1.80530.20471340.16662701X-RAY DIFFRACTION100
1.8053-1.83640.21781400.15712627X-RAY DIFFRACTION100
1.8364-1.86980.20121310.16012664X-RAY DIFFRACTION100
1.8698-1.90580.19061530.15762631X-RAY DIFFRACTION100
1.9058-1.94470.20191320.16472655X-RAY DIFFRACTION100
1.9447-1.9870.20051380.15032662X-RAY DIFFRACTION100
1.987-2.03320.20491700.15022635X-RAY DIFFRACTION100
2.0332-2.0840.17061360.15332674X-RAY DIFFRACTION100
2.084-2.14040.20191250.15052631X-RAY DIFFRACTION100
2.1404-2.20330.19161260.14842679X-RAY DIFFRACTION100
2.2033-2.27440.16451390.14162660X-RAY DIFFRACTION100
2.2744-2.35570.17821710.14912634X-RAY DIFFRACTION100
2.3557-2.450.181430.15062650X-RAY DIFFRACTION100
2.45-2.56150.18761430.15312652X-RAY DIFFRACTION100
2.5615-2.69650.18591400.16042660X-RAY DIFFRACTION100
2.6965-2.86540.22361260.15962687X-RAY DIFFRACTION100
2.8654-3.08660.17781510.16192642X-RAY DIFFRACTION100
3.0866-3.3970.15471400.15472671X-RAY DIFFRACTION99
3.397-3.88820.18961520.14062650X-RAY DIFFRACTION99
3.8882-4.89730.13551350.12712672X-RAY DIFFRACTION99
4.8973-50.17041430.14772724X-RAY DIFFRACTION100

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