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- PDB-8p7t: The impact of molecular variants, crystallization conditions and ... -

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Basic information

Entry
Database: PDB / ID: 8p7t
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
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: 1.8 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: 6G0M
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)37,19916
Polymers35,8071
Non-polymers1,39215
Water4,738263
1
A: Parathion hydrolase
hetero molecules

A: Parathion hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,39732
Polymers71,6132
Non-polymers2,78430
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_465y-1,x+1,-z1
Buried area8720 Å2
ΔGint-209 kcal/mol
Surface area22480 Å2
MethodPISA
Unit cell
Length a, b, c (Å)69.450, 69.450, 186.970
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: 35806.605 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, 278 molecules

#2: Chemical ChemComp-FMT / FORMIC ACID


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


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#4: Chemical ChemComp-VX / O-ETHYLMETHYLPHOSPHONIC ACID ESTER GROUP


Mass: 124.076 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H9O3P / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-E8N / 1-ethyl-1-methyl-cyclohexane


Mass: 126.239 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H18
#6: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


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


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 263 / 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: 3.15 Å3/Da / Density % sol: 60.93 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5 / Details: 1.5M (NH4)2SO4 17% Glycerol 0.1M Tris pH=8.5

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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: Sep 16, 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: 45114 / % possible obs: 97.23 % / Redundancy: 20 % / CC1/2: 0.999 / Rpim(I) all: 0.02038 / Net I/σ(I): 22.59
Reflection shellResolution: 1.8→1.86 Å / Mean I/σ(I) obs: 5.53 / Num. unique obs: 4018 / CC1/2: 0.948 / Rpim(I) all: 0.1358

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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: 1.8→23.192 Å / SU ML: 0.15 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 16.53 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1837 2061 4.88 %
Rwork0.1586 --
obs0.1598 42211 97.3 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.8→23.192 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2488 0 78 263 2829
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0062634
X-RAY DIFFRACTIONf_angle_d0.8673573
X-RAY DIFFRACTIONf_dihedral_angle_d3.6642103
X-RAY DIFFRACTIONf_chiral_restr0.054414
X-RAY DIFFRACTIONf_plane_restr0.005454
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8-1.84190.2071140.18112555X-RAY DIFFRACTION95
1.8419-1.88790.22851330.16452578X-RAY DIFFRACTION95
1.8879-1.93890.19251170.16132601X-RAY DIFFRACTION96
1.9389-1.9960.17481320.15572578X-RAY DIFFRACTION96
1.996-2.06040.17761430.15372603X-RAY DIFFRACTION96
2.0604-2.13390.17721420.15312618X-RAY DIFFRACTION96
2.1339-2.21930.21121360.1522627X-RAY DIFFRACTION97
2.2193-2.32020.20381460.15212645X-RAY DIFFRACTION97
2.3202-2.44240.19331240.15592658X-RAY DIFFRACTION98
2.4424-2.59530.17611270.16262701X-RAY DIFFRACTION98
2.5953-2.79530.19461640.16882675X-RAY DIFFRACTION98
2.7953-3.07610.18081530.16662715X-RAY DIFFRACTION99
3.0761-3.51990.18451340.16462782X-RAY DIFFRACTION99
3.5199-4.42960.16141460.14262810X-RAY DIFFRACTION100
4.4296-100.17631500.16193004X-RAY DIFFRACTION100

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