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- PDB-8p7n: The impact of molecular variants, crystallization conditions and ... -

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Basic information

Entry
Database: PDB / ID: 8p7n
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 / Parathion hydrolase
Similarity search - Component
Biological speciesBrevundimonas diminuta (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.2 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
SupersessionOct 25, 2023ID: 6FU0
Revision 1.0Oct 25, 2023Provider: repository / Type: Initial release
Revision 2.0Nov 1, 2023Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Other / Polymer sequence / Source and taxonomy / Structure summary
Category: atom_site / cell ...atom_site / cell / citation / citation_author / entity / entity_name_com / entity_poly / entity_poly_seq / entity_src_nat / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_poly_seq_scheme / pdbx_unobs_or_zero_occ_residues / struct_asym / struct_ref / struct_ref_seq
Item: _atom_site.label_entity_id / _cell.Z_PDB ..._atom_site.label_entity_id / _cell.Z_PDB / _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 / _pdbx_entity_nonpoly.entity_id / _pdbx_nonpoly_scheme.entity_id / _struct_asym.entity_id / _struct_ref_seq.db_align_end / _struct_ref_seq.pdbx_auth_seq_align_end / _struct_ref_seq.ref_id / _struct_ref_seq.seq_align_end
Revision 2.1Nov 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

Downloads & links

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Assembly

Deposited unit
A: Parathion hydrolase
B: Parathion hydrolase
C: Parathion hydrolase
D: Parathion hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)142,67216
Polymers141,9654
Non-polymers70712
Water724
1
A: Parathion hydrolase
B: Parathion hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,3368
Polymers70,9832
Non-polymers3546
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3420 Å2
ΔGint-166 kcal/mol
Surface area23310 Å2
MethodPISA
2
C: Parathion hydrolase
D: Parathion hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,3368
Polymers70,9832
Non-polymers3546
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3400 Å2
ΔGint-168 kcal/mol
Surface area23100 Å2
MethodPISA
Unit cell
Length a, b, c (Å)88.890, 119.900, 161.490
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
Parathion hydrolase / Phosphotriesterase / PTE


Mass: 35491.254 Da / Num. of mol.: 4
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.: 4 / Source method: isolated from a natural source / Formula: CH2O2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 8 / Source method: isolated from a natural source / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 4 / 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: 3.05 Å3/Da / Density % sol: 59.61 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 10% PEG 6,000 2% PEG 400 15% 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 325 mm CCD / Detector: CCD / Date: Dec 4, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 3.2→77.872 Å / Num. obs: 29131 / % possible obs: 99.61 % / Redundancy: 4.1 % / CC1/2: 0.987 / Rpim(I) all: 0.09627 / Net I/σ(I): 7.24
Reflection shellResolution: 3.2→3.31 Å / Mean I/σ(I) obs: 2.64 / Num. unique obs: 2870 / CC1/2: 0.823 / Rpim(I) all: 0.3261

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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: 3.2→77.872 Å / SU ML: 0.41 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 27.93 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.256 1412 4.86 %
Rwork0.1821 --
obs0.1858 29064 99.62 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.2→77.872 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9874 0 5 4 9883
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0110083
X-RAY DIFFRACTIONf_angle_d1.20513701
X-RAY DIFFRACTIONf_dihedral_angle_d4.2118194
X-RAY DIFFRACTIONf_chiral_restr0.0651617
X-RAY DIFFRACTIONf_plane_restr0.0091770
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.2-3.31440.3491480.2412719X-RAY DIFFRACTION100
3.3144-3.44710.33271130.22152738X-RAY DIFFRACTION100
3.4471-3.6040.30771440.22292721X-RAY DIFFRACTION100
3.604-3.7940.28861200.19512742X-RAY DIFFRACTION100
3.794-4.03170.23351490.18342757X-RAY DIFFRACTION100
4.0317-4.34290.28691200.17232750X-RAY DIFFRACTION100
4.3429-4.77990.26241430.16252770X-RAY DIFFRACTION100
4.7799-5.47150.2271450.15992780X-RAY DIFFRACTION100
5.4715-6.89280.25081640.19322779X-RAY DIFFRACTION99
6.8928-100.17081660.1452896X-RAY DIFFRACTION99

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