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- PDB-8p7q: The impact of molecular variants, crystallization conditions and ... -

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Basic information

Entry
Database: PDB / ID: 8p7q
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 / propan-2-yl hydrogen (S)-methylphosphonate / Parathion hydrolase
Similarity search - Component
Biological speciesBrevundimonas diminuta (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.77 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: 6FVK
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

Downloads & links

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Assembly

Deposited unit
A: Parathion hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,81212
Polymers35,8071
Non-polymers1,00611
Water4,648258
1
A: Parathion hydrolase
hetero molecules

A: Parathion hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,62524
Polymers71,6132
Non-polymers2,01122
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Buried area5400 Å2
ΔGint-70 kcal/mol
Surface area22560 Å2
MethodPISA
Unit cell
Length a, b, c (Å)69.560, 69.560, 186.640
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, 269 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-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3 / 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 / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical ChemComp-UCJ / propan-2-yl hydrogen (S)-methylphosphonate


Mass: 138.102 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H11O3P / Feature type: SUBJECT OF INVESTIGATION
#7: Chemical ChemComp-SO4 / SULFATE ION


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


Mass: 18.015 Da / Num. of mol.: 258 / 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: 60.98 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: 1.5M (NH4)2SO4 17% Glycerol 0.1M Tris pH=7.0

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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: May 22, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.541 Å / Relative weight: 1
ReflectionResolution: 1.77→34.8 Å / Num. obs: 45349 / % possible obs: 99.92 % / Redundancy: 20 % / CC1/2: 0.999 / Rpim(I) all: 0.02413 / Net I/σ(I): 18.97
Reflection shellResolution: 1.77→1.87 Å / Mean I/σ(I) obs: 6.41 / Num. unique obs: 4453 / CC1/2: 0.974 / Rpim(I) all: 0.0978

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Processing

Software
NameVersionClassification
REFMAC5.8.0266refinement
HKL-3000data reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.77→34.8 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.954 / SU B: 1.444 / SU ML: 0.047 / Cross valid method: THROUGHOUT / ESU R: 0.085 / ESU R Free: 0.086 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.186 2285 5 %RANDOM
Rwork0.157 ---
obs0.158 43061 99.9 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 17.59 Å2
Baniso -1Baniso -2Baniso -3
1-0.33 Å20 Å20 Å2
2--0.33 Å20 Å2
3----0.67 Å2
Refinement stepCycle: LAST / Resolution: 1.77→34.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2490 0 55 258 2803
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0132643
X-RAY DIFFRACTIONr_bond_other_d0.0030.0182535
X-RAY DIFFRACTIONr_angle_refined_deg1.9921.6493587
X-RAY DIFFRACTIONr_angle_other_deg1.6911.6065800
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.1885339
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.23219.852135
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.56615419
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.6771527
X-RAY DIFFRACTIONr_chiral_restr0.1690.2361
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.023010
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02623
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.531.631344
X-RAY DIFFRACTIONr_mcbond_other1.531.6291345
X-RAY DIFFRACTIONr_mcangle_it2.1792.4381687
X-RAY DIFFRACTIONr_mcangle_other2.1852.441688
X-RAY DIFFRACTIONr_scbond_it2.8821.9591299
X-RAY DIFFRACTIONr_scbond_other2.7951.9281288
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.0762.7771883
X-RAY DIFFRACTIONr_long_range_B_refined5.41220.9263059
X-RAY DIFFRACTIONr_long_range_B_other5.13520.5583007
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.77→1.82 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.208 170 -
Rwork0.179 3129 -
obs--100 %

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