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- PDB-8p7k: The impact of molecular variants, crystallization conditions and ... -

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Basic information

Entry
Database: PDB / ID: 8p7k
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
(2~{R})-2-methylpentanedioic acid / FORMIC ACID / Parathion hydrolase
Similarity search - Component
Biological speciesBrevundimonas diminuta (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.929 Å
AuthorsDym, O. / Aggawal, 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
SupersessionJun 7, 2023ID: 6FEV
Revision 1.0Jun 7, 2023Provider: repository / Type: Initial release
Revision 1.1Nov 1, 2023Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_id_CSD ..._citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
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
B: Parathion hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,15910
Polymers73,5132
Non-polymers6468
Water8,341463
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3040 Å2
ΔGint-60 kcal/mol
Surface area23330 Å2
Unit cell
Length a, b, c (Å)55.034, 81.488, 70.810
Angle α, β, γ (deg.)90.00, 95.00, 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 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-E5N / (2~{R})-2-methylpentanedioic acid


Mass: 146.141 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H10O4 / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 463 / 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: 2.2 Å3/Da / Density % sol: 43.97 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 22% Polyacrylic acid 0.02M MgCl2 0.1M HEPES 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: Jul 28, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.541 Å / Relative weight: 1
ReflectionResolution: 1.929→32.702 Å / Num. obs: 46379 / % possible obs: 98.69 % / Redundancy: 3.5 % / CC1/2: 0.995 / Rpim(I) all: 0.052 / Net I/σ(I): 10.8
Reflection shellResolution: 1.93→2 Å / Mean I/σ(I) obs: 2.9 / Num. unique obs: 4410 / CC1/2: 0.772 / Rpim(I) all: 0.338

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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: 1.929→32.702 Å / SU ML: 0.23 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 21.89 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2122 2355 5.08 %
Rwork0.1595 --
obs0.1621 46365 98.71 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.929→32.702 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4991 0 30 463 5484
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0075132
X-RAY DIFFRACTIONf_angle_d0.8266972
X-RAY DIFFRACTIONf_dihedral_angle_d3.7824170
X-RAY DIFFRACTIONf_chiral_restr0.049816
X-RAY DIFFRACTIONf_plane_restr0.005907
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.929-1.96830.30811330.23352377X-RAY DIFFRACTION91
1.9683-2.01110.2771190.21752533X-RAY DIFFRACTION98
2.0111-2.05790.30071370.21222572X-RAY DIFFRACTION98
2.0579-2.10930.25151540.1912568X-RAY DIFFRACTION98
2.1093-2.16630.23311660.1812544X-RAY DIFFRACTION99
2.1663-2.23010.25631250.17182590X-RAY DIFFRACTION99
2.2301-2.3020.22021390.16862585X-RAY DIFFRACTION99
2.302-2.38430.20391390.1642599X-RAY DIFFRACTION99
2.3843-2.47970.23041330.16682589X-RAY DIFFRACTION99
2.4797-2.59250.22341290.16162625X-RAY DIFFRACTION100
2.5925-2.72920.21451380.1632613X-RAY DIFFRACTION100
2.7292-2.90.22551510.16712615X-RAY DIFFRACTION100
2.9-3.12380.23261340.1712603X-RAY DIFFRACTION100
3.1238-3.43780.23271180.17142662X-RAY DIFFRACTION100
3.4378-3.93460.19881190.14472664X-RAY DIFFRACTION100
3.9346-4.95440.16931820.12242591X-RAY DIFFRACTION100
4.9544-5.50.16721390.13662680X-RAY DIFFRACTION99

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