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- PDB-8anu: Crystal structure of protein phi3T-93 -

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Basic information

Entry
Database: PDB / ID: 8anu
TitleCrystal structure of protein phi3T-93
ComponentsYopN. Phi3T_93
KeywordsVIRAL PROTEIN / Arbitrium / Phi3T / lysis-lysogeny decission
Function / homologymetal ion binding / NICKEL (II) ION / Uncharacterized protein
Function and homology information
Biological speciesBacillus phage phi3T (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.31014705408 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
C: YopN. Phi3T_93
A: YopN. Phi3T_93
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,6534
Polymers19,5362
Non-polymers1172
Water64936
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4170 Å2
ΔGint-39 kcal/mol
Surface area8770 Å2
MethodPISA
Unit cell
Length a, b, c (Å)46.3497, 49.9101, 70.5299
Angle α, β, γ (deg.)90.0, 107.737, 90.0
Int Tables number5
Space group name H-MI121
Space group name HallC2y(x,y,-x+z)
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z+1/2
#4: -x+1/2,y+1/2,-z+1/2
Components on special symmetry positions
IDModelComponents
11C-101-

NI

21A-101-

NI

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11METMETASNASNchain 'A'AB1 - 42 - 5
12TYRTYRILEILEchain 'A'AB6 - 317 - 32
13GLUGLULEULEUchain 'A'AB33 - 3634 - 37
14TYRTYRASNASNchain 'A'AB38 - 6639 - 67
21METMETASNASNchain 'C'CA1 - 42 - 5
22TYRTYRILEILEchain 'C'CA6 - 317 - 32
23GLUGLULEULEUchain 'C'CA33 - 3634 - 37
24TYRTYRASNASNchain 'C'CA38 - 6639 - 67

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Components

#1: Protein YopN. Phi3T_93


Mass: 9768.052 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) / Strain (production host): BL21 RIL / References: UniProt: A0A1P8CWW1
#2: Chemical ChemComp-NI / NICKEL (II) ION


Mass: 58.693 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ni / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 36 / 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: 1.99 Å3/Da / Density % sol: 38.15 %
Crystal growTemperature: 294.15 K / Method: vapor diffusion, sitting drop
Details: 10%PEG8000, 50mM magnesium acetate, 100mM sodium acetate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.97918 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 28, 2021
RadiationMonochromator: Channel-cut Si (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 2.31→43.47 Å / Num. obs: 6697 / % possible obs: 98.1 % / Redundancy: 4.9 % / Biso Wilson estimate: 33.4114979572 Å2 / CC1/2: 0.993 / Rmerge(I) obs: 0.1 / Net I/σ(I): 8.5
Reflection shellResolution: 2.31→2.44 Å / Redundancy: 5.1 % / Rmerge(I) obs: 0.212 / Mean I/σ(I) obs: 4.4 / Num. unique obs: 985 / CC1/2: 0.961 / Rpim(I) all: 0.102 / Rrim(I) all: 0.237 / % possible all: 98.6

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
iMOSFLMdata reduction
SCALAdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 8ANT

8ant


Resolution: 2.31014705408→40.06302883 Å / SU ML: 0.252471672262 / Cross valid method: FREE R-VALUE / σ(F): 1.33786559852 / Phase error: 28.1250642639
RfactorNum. reflection% reflection
Rfree0.26035485716 333 5.01128668172 %
Rwork0.209155328901 6312 -
obs0.211675325209 6645 97.149122807 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 38.1353823492 Å2
Refinement stepCycle: LAST / Resolution: 2.31014705408→40.06302883 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1126 0 2 37 1165
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01020087159411166
X-RAY DIFFRACTIONf_angle_d1.159361243891577
X-RAY DIFFRACTIONf_chiral_restr0.0501588705662160
X-RAY DIFFRACTIONf_plane_restr0.00604595465445203
X-RAY DIFFRACTIONf_dihedral_angle_d15.8767808162430
LS refinement shellResolution: 2.31015→2.9104 Å
RfactorNum. reflection% reflection
Rfree0.274579341634 170 -
Rwork0.23914571553 3136 -
obs--97.3498233216 %

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