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- PDB-8ju3: Mu phage tail fiber -

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Basic information

Entry
Database: PDB / ID: 8ju3
TitleMu phage tail fiber
ComponentsTail fiber protein S,Tail fiber protein S'
KeywordsVIRAL PROTEIN / bacteriophage
Function / homology
Function and homology information


viral tropism switching / virus tail, fiber / adhesion receptor-mediated virion attachment to host cell / host cell cytoplasm / symbiont entry into host cell
Similarity search - Function
Bacteriophage lambda, Tail fiber protein, repeat-2 / Phage tail fibre repeat / : / Long-tail fiber proximal subunit, C-terminal, trimerization domain / : / Bacteriophage T7, Gp17, C-terminal / Tail fibre protein gp37 C terminal domain
Similarity search - Domain/homology
Tail fiber protein S' / Tail fiber protein S
Similarity search - Component
Biological speciesEscherichia phage Mu (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsYamashita, E. / Takeda, S.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Virology / Year: 2024
Title: Determination of the three-dimensional structure of bacteriophage Mu(-) tail fiber and its characterization.
Authors: Mori, Y. / Yamashita, E. / Nakagawa, A. / Matsuzawa, T. / Inagaki, M. / Aiba, Y. / Tanaka, S. / Hatori, S. / Ayami, M. / Takeda, S.
History
DepositionJun 24, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 28, 2024Provider: repository / Type: Initial release
Revision 1.1Sep 11, 2024Group: 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.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: Tail fiber protein S,Tail fiber protein S'


Theoretical massNumber of molelcules
Total (without water)52,6971
Polymers52,6971
Non-polymers00
Water4,179232
1
A: Tail fiber protein S,Tail fiber protein S'

A: Tail fiber protein S,Tail fiber protein S'

A: Tail fiber protein S,Tail fiber protein S'


Theoretical massNumber of molelcules
Total (without water)158,0923
Polymers158,0923
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_565-y,x-y+1,z1
crystal symmetry operation3_455-x+y-1,-x,z1
Buried area21880 Å2
ΔGint-152 kcal/mol
Surface area30570 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.839, 63.839, 462.383
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number150
Space group name H-MP321
Space group name HallP32"
Symmetry operation#1: x,y,z
#2: -y,x-y,z
#3: -x+y,-x,z
#4: x-y,-y,-z
#5: -x,-x+y,-z
#6: y,x,-z
Components on special symmetry positions
IDModelComponents
11A-506-

HOH

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Components

#1: Protein Tail fiber protein S,Tail fiber protein S' / Gene product 49 / gp49 / Gene product S / gpS / Gene product S' / gpS'


Mass: 52697.312 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia phage Mu (virus) / Gene: S, Mup49, S', Mup52
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
Variant (production host): pLysS / References: UniProt: Q9T1V0, UniProt: P0DJY6
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 232 / 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: 5.16 Å3/Da / Density % sol: 76.17 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 0.1M HEPES (pH 7.5), 4.3M NaCl

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 0.9 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Oct 27, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 2→49.88 Å / Num. obs: 76418 / % possible obs: 99.75 % / Redundancy: 9.39 % / Biso Wilson estimate: 36.52 Å2 / CC1/2: 0.996 / Net I/σ(I): 8.4
Reflection shellResolution: 2→2.03 Å / Num. unique obs: 3548 / CC1/2: 0.611

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→49.88 Å / SU ML: 0.1994 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 18.5094
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2149 3722 4.87 %
Rwork0.1976 72642 -
obs0.1984 76364 99.68 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 65.37 Å2
Refinement stepCycle: LAST / Resolution: 2→49.88 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2203 0 0 232 2435
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01942258
X-RAY DIFFRACTIONf_angle_d1.35743074
X-RAY DIFFRACTIONf_chiral_restr0.1166322
X-RAY DIFFRACTIONf_plane_restr0.016402
X-RAY DIFFRACTIONf_dihedral_angle_d6.782317
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.020.33171120.26812422X-RAY DIFFRACTION93.44
2.02-2.050.24611720.23972681X-RAY DIFFRACTION99.96
2.05-2.080.18171270.21822630X-RAY DIFFRACTION100
2.08-2.110.24991160.21342634X-RAY DIFFRACTION100
2.11-2.140.23141470.20592692X-RAY DIFFRACTION99.96
2.14-2.170.21671460.1962594X-RAY DIFFRACTION100
2.17-2.210.23661610.20552664X-RAY DIFFRACTION99.96
2.21-2.250.20731340.19942598X-RAY DIFFRACTION99.93
2.25-2.290.22021500.18532691X-RAY DIFFRACTION99.93
2.29-2.330.19861330.18252598X-RAY DIFFRACTION100
2.33-2.380.17441480.17372699X-RAY DIFFRACTION99.96
2.38-2.430.19461210.1762635X-RAY DIFFRACTION99.96
2.43-2.490.21851220.17442685X-RAY DIFFRACTION99.86
2.49-2.550.18281690.17052670X-RAY DIFFRACTION99.93
2.55-2.620.18521490.19532618X-RAY DIFFRACTION99.89
2.62-2.690.22291430.19632683X-RAY DIFFRACTION99.96
2.69-2.780.22051100.21542768X-RAY DIFFRACTION99.97
2.78-2.880.22311580.21442620X-RAY DIFFRACTION100
2.88-30.22361130.19842721X-RAY DIFFRACTION99.93
3-3.130.21991380.19162698X-RAY DIFFRACTION100
3.13-3.30.16751140.18142736X-RAY DIFFRACTION100
3.3-3.50.19071390.17582726X-RAY DIFFRACTION99.93
3.5-3.770.18641310.16842769X-RAY DIFFRACTION99.97
3.77-4.150.19281100.1732737X-RAY DIFFRACTION99.86
4.15-4.750.1921200.16912815X-RAY DIFFRACTION99.83
4.75-5.990.20421590.21052819X-RAY DIFFRACTION99.83
5.99-49.880.3031800.28083039X-RAY DIFFRACTION99.32
Refinement TLS params.Method: refined / Origin x: -30.6839202554 Å / Origin y: 10.5883412353 Å / Origin z: 33.6374153333 Å
111213212223313233
T0.297946291113 Å2-8.56430837814E-5 Å20.0188633559631 Å2-0.286204414883 Å20.0344213217971 Å2--0.329507312381 Å2
L0.635164021429 °20.0112275587699 °20.170480777126 °2-0.683158897107 °20.127508807153 °2--1.12310998605 °2
S0.00805620813617 Å °-0.355600972121 Å °-0.0912716211115 Å °0.385587812809 Å °-0.028666745671 Å °0.0210193488373 Å °0.191887049555 Å °-0.0773222083087 Å °-0.00207088398231 Å °
Refinement TLS groupSelection details: all

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