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- PDB-8ant: Crystal structure of 6xhis-tagged phi3T_93 protein -

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Basic information

Entry
Database: PDB / ID: 8ant
TitleCrystal structure of 6xhis-tagged phi3T_93 protein
ComponentsYopN, Phi3T_93
KeywordsVIRAL PROTEIN / Arbitrium / Phi3T / lysis-lysogeny decission
Function / homologymetal ion binding / Uncharacterized protein
Function and homology information
Biological speciesBacillus phage phi3T (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / AB INITIO PHASING / Resolution: 1.9 Å
AuthorsZamora-Caballero, S. / Marina, A.
Funding support Spain, 1items
OrganizationGrant numberCountry
Ministerio de Ciencia e Innovacion (MCIN)PID2019-108541GB-100 Spain
CitationJournal: Nat Microbiol / Year: 2024
Title: Antagonistic interactions between phage and host factors control arbitrium lysis-lysogeny decision.
Authors: Zamora-Caballero, S. / Chmielowska, C. / Quiles-Puchalt, N. / Brady, A. / Del Sol, F.G. / Mancheno-Bonillo, J. / Felipe-Ruiz, A. / Meijer, W.J.J. / Penades, J.R. / Marina, A.
History
DepositionAug 5, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 25, 2023Provider: repository / Type: Initial release
Revision 1.1Jan 17, 2024Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: YopN, Phi3T_93
B: YopN, Phi3T_93


Theoretical massNumber of molelcules
Total (without water)24,4792
Polymers24,4792
Non-polymers00
Water79344
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5250 Å2
ΔGint-41 kcal/mol
Surface area9760 Å2
MethodPISA
Unit cell
Length a, b, c (Å)37.150, 50.828, 55.804
Angle α, β, γ (deg.)90.000, 101.960, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1(chain "A" and (resid -10 through -2 or resid 0...
d_2ens_1(chain "B" and (resid -10 through -2 or resid 0...

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg label comp-IDEnd label comp-IDLabel asym-IDLabel seq-ID
d_11ens_1ASPPHEA1 - 9
d_12ens_1SERILEA11 - 32
d_13ens_1LEULEUA34 - 47
d_14ens_1TYRASNA49 - 56
d_15ens_1GLUGLYA58 - 79
d_21ens_1ASPPHEB1 - 9
d_22ens_1SERILEB11 - 32
d_23ens_1LEULEUB34 - 47
d_24ens_1TYRASNB49 - 56
d_25ens_1GLUGLYB58 - 79

NCS oper: (Code: givenMatrix: (-0.999998999312, -0.00131241290325, 0.000528155320264), (-0.00126968177914, 0.997251556147, 0.0740791581419), (-0.000623926158028, 0.0740784134226, -0.997252224556) ...NCS oper: (Code: given
Matrix: (-0.999998999312, -0.00131241290325, 0.000528155320264), (-0.00126968177914, 0.997251556147, 0.0740791581419), (-0.000623926158028, 0.0740784134226, -0.997252224556)
Vector: -31.1440976737, 1.04508105047, -28.2776065172)

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Components

#1: Protein YopN, Phi3T_93


Mass: 12239.717 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus phage phi3T (virus) / Gene: phi3T_93 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A1P8CWW1
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 44 / Source method: isolated from a natural source / Formula: H2O

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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: 2.11 Å3/Da / Density % sol: 41.58 %
Crystal growTemperature: 294.15 K / Method: vapor diffusion, sitting drop / pH: 8 / Details: 0.1M Tris pH8, 5% glycerol, 0.6M Na/K tartrate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.97925 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 17, 2021
RadiationMonochromator: Channel-cut Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97925 Å / Relative weight: 1
ReflectionResolution: 1.9→50.83 Å / Num. obs: 16124 / % possible obs: 99.7 % / Redundancy: 6 % / Biso Wilson estimate: 34.06 Å2 / CC1/2: 0.995 / Rmerge(I) obs: 0.081 / Net I/σ(I): 8
Reflection shellResolution: 1.9→1.94 Å / Rmerge(I) obs: 0.382 / Num. unique obs: 1017 / CC1/2: 0.975 / % possible all: 98.8

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Processing

Software
NameVersionClassification
PHENIX1.20_4459refinement
DIALSdata reduction
Aimlessdata scaling
Arcimboldophasing
RefinementMethod to determine structure: AB INITIO PHASING / Resolution: 1.9→37.2 Å / SU ML: 0.2875 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 32.7673
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2489 803 5.01 %
Rwork0.2165 15106 -
obs0.2181 15902 98.29 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 44.9 Å2
Refinement stepCycle: LAST / Resolution: 1.9→37.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1346 0 0 44 1390
Refine LS restraintsType: f_dihedral_angle_d / Dev ideal: 5.6902 / Number: 179
Refine LS restraints NCSType: Torsion NCS / Rms dev position: 0.491121930325 Å
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9-2.020.33341250.34162478X-RAY DIFFRACTION97.34
2.02-2.170.31011540.27712461X-RAY DIFFRACTION97.72
2.18-2.390.28191280.23442483X-RAY DIFFRACTION98.05
2.39-2.740.27321200.23452548X-RAY DIFFRACTION98.71
2.74-3.450.31991400.22562544X-RAY DIFFRACTION99

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