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- PDB-5yvq: Complex of Mu phage tail fiber and its chaperone -

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Basic information

Entry
Database: PDB / ID: 5yvq
TitleComplex of Mu phage tail fiber and its chaperone
Components
  • Tail fiber assembly protein U
  • Tail fiber protein S
KeywordsVIRAL PROTEIN / bacteriophage
Function / homology
Function and homology information


viral tropism switching / virus tail fiber assembly / virus tail, fiber / adhesion receptor-mediated virion attachment to host cell / host cell cytoplasm / symbiont entry into host cell
Similarity search - Function
Bacteriophage T4, Gp38, tail fibre assembly / : / Caudovirales tail fibre assembly protein, lambda gpK / Bacteriophage lambda, Tail fiber protein, repeat-2 / Phage tail fibre repeat / : / : / Long-tail fiber proximal subunit, C-terminal, trimerization domain
Similarity search - Domain/homology
Tail fiber assembly protein U / Tail fiber protein S
Similarity search - Component
Biological speciesEscherichia phage Mu (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.103 Å
AuthorsTakeda, S. / Sakai, K. / Iwazaki, T. / Yamashita, E. / Nakagawa, A.
CitationJournal: Nat Microbiol / Year: 2019
Title: Phage tail fibre assembly proteins employ a modular structure to drive the correct folding of diverse fibres.
Authors: North, O.I. / Sakai, K. / Yamashita, E. / Nakagawa, A. / Iwazaki, T. / Buttner, C.R. / Takeda, S. / Davidson, A.R.
History
DepositionNov 27, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 22, 2019Provider: repository / Type: Initial release
Revision 1.1Oct 9, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _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 / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Mar 27, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Tail fiber protein S
B: Tail fiber assembly protein U
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,2067
Polymers75,7452
Non-polymers4605
Water7,476415
1
A: Tail fiber protein S
B: Tail fiber assembly protein U
hetero molecules

A: Tail fiber protein S
B: Tail fiber assembly protein U
hetero molecules

A: Tail fiber protein S
B: Tail fiber assembly protein U
hetero molecules


Theoretical massNumber of molelcules
Total (without water)228,61721
Polymers227,2356
Non-polymers1,38115
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-y+1,x-y,z1
crystal symmetry operation3_665-x+y+1,-x+1,z1
Unit cell
Length a, b, c (Å)66.332, 66.332, 387.769
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number150
Space group name H-MP321
Components on special symmetry positions
IDModelComponents
11A-787-

HOH

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Components

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


Mass: 55412.551 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia phage Mu (virus) / Gene: S, Mup49 / Plasmid: pET21a-LIC / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): pLysS / References: UniProt: Q9T1V0
#2: Protein Tail fiber assembly protein U / Gene product 50 / gp50 / Gene product U / gpU


Mass: 20332.594 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia phage Mu (virus) / Gene: U, Mup50 / Plasmid: pET21a-LIC / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): pLysS / References: UniProt: Q9T1U9
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 415 / 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: 3.25 Å3/Da / Density % sol: 62.17 %
Crystal growTemperature: 298 K / Method: evaporation / Details: (NH4)2SO4, 2-Methyl-2,4-pentanediol

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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: RAYONIX MX300HE / Detector: CCD / Date: Apr 5, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 2.1→50 Å / Num. obs: 59378 / % possible obs: 99.9 % / Redundancy: 9 % / Rmerge(I) obs: 0.164 / Rpim(I) all: 0.073 / Rrim(I) all: 0.174 / Net I/σ(I): 14.3
Reflection shellResolution: 2.1→2.14 Å / Redundancy: 9.2 % / Mean I/σ(I) obs: 1.8 / CC1/2: 0.741 / Rpim(I) all: 0.624 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
SHARPphasing
RefinementMethod to determine structure: MAD / Resolution: 2.103→32.14 Å / SU ML: 0.26 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 26.03
RfactorNum. reflection% reflection
Rfree0.2638 2965 5.01 %
Rwork0.2365 --
obs0.2378 59229 99.55 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.103→32.14 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3629 0 30 415 4074
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0083755
X-RAY DIFFRACTIONf_angle_d0.8435077
X-RAY DIFFRACTIONf_dihedral_angle_d2.9553049
X-RAY DIFFRACTIONf_chiral_restr0.058536
X-RAY DIFFRACTIONf_plane_restr0.005666
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1028-2.13730.33421640.28912635X-RAY DIFFRACTION98
2.1373-2.17420.28461670.28882514X-RAY DIFFRACTION99
2.1742-2.21370.37341590.32042669X-RAY DIFFRACTION100
2.2137-2.25620.36161220.36912605X-RAY DIFFRACTION100
2.2562-2.30230.34831510.32292660X-RAY DIFFRACTION100
2.3023-2.35230.32111390.28292607X-RAY DIFFRACTION100
2.3523-2.4070.29091390.25082624X-RAY DIFFRACTION100
2.407-2.46720.27841150.21952691X-RAY DIFFRACTION100
2.4672-2.53390.26841430.21882630X-RAY DIFFRACTION100
2.5339-2.60840.26921470.21782630X-RAY DIFFRACTION100
2.6084-2.69260.23071360.21722650X-RAY DIFFRACTION100
2.6926-2.78880.19781290.20542708X-RAY DIFFRACTION100
2.7888-2.90030.2471490.20012668X-RAY DIFFRACTION100
2.9003-3.03230.24031540.19952677X-RAY DIFFRACTION100
3.0323-3.1920.2331490.20872661X-RAY DIFFRACTION100
3.192-3.39180.26721330.20542685X-RAY DIFFRACTION100
3.3918-3.65330.26791120.19662714X-RAY DIFFRACTION99
3.6533-4.02030.21561080.20212728X-RAY DIFFRACTION100
4.0203-4.60060.21071390.18882764X-RAY DIFFRACTION99
4.6006-5.79080.24971440.21592782X-RAY DIFFRACTION99
5.7908-32.14360.30171660.33392962X-RAY DIFFRACTION99
Refinement TLS params.Method: refined / Origin x: 37.7485 Å / Origin y: 18.5873 Å / Origin z: 208.2416 Å
111213212223313233
T0.0733 Å20.0167 Å2-0.0162 Å2-0.1058 Å20.0141 Å2--0.1445 Å2
L0.1494 °20.0104 °2-0.1086 °2-0.1732 °20.1027 °2--1.4676 °2
S-0.0358 Å °-0.0204 Å °-0.0062 Å °0.0332 Å °-0.0281 Å °-0.0269 Å °0.0641 Å °0.2191 Å °-0.004 Å °
Refinement TLS groupSelection details: all

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