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- PDB-6gap: Crystal structure of the T3D reovirus sigma1 coiled coil tail and body -

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Basic information

Entry
Database: PDB / ID: 6gap
TitleCrystal structure of the T3D reovirus sigma1 coiled coil tail and body
ComponentsOuter capsid protein sigma-1
KeywordsVIRAL PROTEIN / cell attachment protein / reovirus sigma1 / coiled coil / beta-spiral repeat
Function / homologyViral attachment sigma 1, reoviral / Reovirus viral attachment protein sigma 1 / Attachment protein shaft domain superfamily / viral outer capsid / Adenovirus pIV-like, attachment domain / cell adhesion / symbiont entry into host cell / virion attachment to host cell / Outer capsid protein sigma-1
Function and homology information
Biological speciesMammalian orthoreovirus 3 Dearing
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.15 Å
AuthorsDietrich, M.H. / Stehle, T.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01 AI118887 United States
CitationJournal: J. Virol. / Year: 2018
Title: Structural and Functional Features of the Reovirus sigma 1 Tail.
Authors: Dietrich, M.H. / Ogden, K.M. / Long, J.M. / Ebenhoch, R. / Thor, A. / Dermody, T.S. / Stehle, T.
History
DepositionApr 11, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 25, 2018Provider: repository / Type: Initial release
Revision 1.1May 9, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_abbrev / _citation.pdbx_database_id_DOI ..._citation.journal_abbrev / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Jul 11, 2018Group: Data collection / Database references / Category: citation / Item: _citation.journal_volume
Revision 1.3Mar 30, 2022Group: Author supporting evidence / Database references / Category: database_2 / pdbx_audit_support
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_audit_support.funding_organization
Revision 1.4Jan 17, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Outer capsid protein sigma-1
B: Outer capsid protein sigma-1
C: Outer capsid protein sigma-1


Theoretical massNumber of molelcules
Total (without water)84,0583
Polymers84,0583
Non-polymers00
Water7,476415
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area25750 Å2
ΔGint-194 kcal/mol
Surface area32370 Å2
MethodPISA
Unit cell
Length a, b, c (Å)350.710, 41.530, 63.320
Angle α, β, γ (deg.)90.00, 94.98, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Outer capsid protein sigma-1 / Sigma1 / Cell attachment protein / Hemagglutinin


Mass: 28019.248 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mammalian orthoreovirus 3 Dearing / Gene: S1 / Production host: Escherichia coli (E. coli) / References: UniProt: P03528
#2: 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: 2.73 Å3/Da / Density % sol: 55.01 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 40% MPD, 0.1M Tris pH 8.0, 3% (w/v) 1,6-diaminohexane

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: May 23, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.15→49.15 Å / Num. obs: 50259 / % possible obs: 99.9 % / Redundancy: 6.8 % / Biso Wilson estimate: 35.47 Å2 / CC1/2: 0.999 / Rrim(I) all: 0.127 / Net I/σ(I): 13.7
Reflection shellResolution: 2.15→2.21 Å / Redundancy: 6.5 % / Mean I/σ(I) obs: 2.3 / Num. unique obs: 3674 / CC1/2: 0.797 / Rrim(I) all: 0.995 / % possible all: 99.8

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Processing

Software
NameVersionClassification
BUSTER2.10.0refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6GAJ

6gaj


Resolution: 2.15→49.15 Å / Cor.coef. Fo:Fc: 0.9146 / Cor.coef. Fo:Fc free: 0.8777 / SU R Cruickshank DPI: 0.187 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.194 / SU Rfree Blow DPI: 0.174 / SU Rfree Cruickshank DPI: 0.172
RfactorNum. reflection% reflectionSelection details
Rfree0.2489 2553 5.08 %RANDOM
Rwork0.2079 ---
obs0.21 50257 99.9 %-
Displacement parametersBiso mean: 48.28 Å2
Baniso -1Baniso -2Baniso -3
1-9.2265 Å20 Å29.7406 Å2
2---1.4423 Å20 Å2
3----7.7842 Å2
Refine analyzeLuzzati coordinate error obs: 0.27 Å
Refinement stepCycle: 1 / Resolution: 2.15→49.15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4771 0 0 415 5186
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.014794HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.036505HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1732SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes145HARMONIC2
X-RAY DIFFRACTIONt_gen_planes708HARMONIC5
X-RAY DIFFRACTIONt_it4794HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion2.74
X-RAY DIFFRACTIONt_other_torsion17.32
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion704SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact5816SEMIHARMONIC4
LS refinement shellResolution: 2.15→2.21 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.3101 204 5.56 %
Rwork0.2439 3462 -
all0.2476 3666 -
obs--99.9 %

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