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- PDB-5ydn: Mu pahge neck subunit -

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Basic information

Entry
Database: PDB / ID: 5ydn
TitleMu pahge neck subunit
ComponentsGene product J
KeywordsVIRAL PROTEIN / bacteriophage / assembly
Function / homologyBacteriophage Mu, Gene product J / Bacteriophage Mu, Gp36 / host cell cytoplasm / Gene product J
Function and homology information
Biological speciesEscherichia virus Mu
MethodX-RAY DIFFRACTION / SYNCHROTRON / SIRAS / Resolution: 1.6 Å
AuthorsTakeda, S. / Iwasaki, T. / Yamashita, E. / Nakagawa, A.
Funding support Japan, 1items
OrganizationGrant numberCountry
Japan
CitationJournal: Genes Cells / Year: 2018
Title: Three-dimensional structures of bacteriophage neck subunits are shared in Podoviridae, Siphoviridae and Myoviridae
Authors: Iwasaki, T. / Yamashita, E. / Nakagawa, A. / Enomoto, A. / Tomihara, M. / Takeda, S.
History
DepositionSep 13, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 11, 2018Provider: repository / Type: Initial release
Revision 1.1Jul 25, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
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

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Assembly

Deposited unit
A: Gene product J


Theoretical massNumber of molelcules
Total (without water)12,2541
Polymers12,2541
Non-polymers00
Water1,51384
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area6260 Å2
Unit cell
Length a, b, c (Å)49.398, 69.643, 68.785
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein Gene product J / gpJ / Gene product 36 / gp36


Mass: 12253.813 Da / Num. of mol.: 1 / Fragment: UNP residues 1-109
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia virus Mu / Gene: J, Mup36 / Production host: Expression vector pET21a-LIC (others) / References: UniProt: Q9T1V9
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 84 / 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: 2.41 Å3/Da / Density % sol: 49.05 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.1M HEPES (pH 7.5), 0.8M sodium phosphate, 0.8M potassium phosphate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 0.9 Å
DetectorType: RAYONIX MX300HE / Detector: CCD / Date: Dec 17, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 1.6→50 Å / Num. obs: 15547 / % possible obs: 97.3 % / Redundancy: 6.6 % / Net I/σ(I): 29.5

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Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
HKL-2000data reduction
HKL-2000data scaling
SHARPphasing
RefinementMethod to determine structure: SIRAS / Resolution: 1.6→34.77 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.952 / SU B: 1.483 / SU ML: 0.052 / Cross valid method: THROUGHOUT / ESU R: 0.085 / ESU R Free: 0.086 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20582 790 5.1 %RANDOM
Rwork0.17499 ---
obs0.1765 14698 97.08 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 33.344 Å2
Baniso -1Baniso -2Baniso -3
1-0.37 Å20 Å20 Å2
2---1.68 Å2-0 Å2
3---1.31 Å2
Refinement stepCycle: 1 / Resolution: 1.6→34.77 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms860 0 0 84 944
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0240.02892
X-RAY DIFFRACTIONr_bond_other_d0.0020.02841
X-RAY DIFFRACTIONr_angle_refined_deg2.3781.9551221
X-RAY DIFFRACTIONr_angle_other_deg1.12231926
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.6855112
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.61723.48843
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.42115142
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.051159
X-RAY DIFFRACTIONr_chiral_restr0.1260.2142
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.0211021
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02208
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it3.6913.031442
X-RAY DIFFRACTIONr_mcbond_other3.6613.021441
X-RAY DIFFRACTIONr_mcangle_it5.514.522553
X-RAY DIFFRACTIONr_mcangle_other5.5144.527554
X-RAY DIFFRACTIONr_scbond_it4.5163.41448
X-RAY DIFFRACTIONr_scbond_other4.5113.415449
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other6.3744.931668
X-RAY DIFFRACTIONr_long_range_B_refined8.6524.8691076
X-RAY DIFFRACTIONr_long_range_B_other8.62424.4761054
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.602→1.644 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.276 63 -
Rwork0.208 1096 -
obs--99.23 %

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