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- PDB-6gaj: Crystal structure of the T1L reovirus sigma1 coiled coil tail (iodide) -

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Basic information

Entry
Database: PDB / ID: 6gaj
TitleCrystal structure of the T1L reovirus sigma1 coiled coil tail (iodide)
ComponentsOuter capsid protein sigma-1
KeywordsVIRAL PROTEIN / cell attachment protein / reovirus sigma1 / coiled coil
Function / homology
Function and homology information


viral outer capsid / viral capsid / cell adhesion / symbiont entry into host cell / virion attachment to host cell
Similarity search - Function
Viral attachment sigma 1, reoviral / Reovirus viral attachment protein sigma 1 / Adenovirus pIV-like, attachment domain
Similarity search - Domain/homology
IODIDE ION / Outer capsid protein sigma-1
Similarity search - Component
Biological speciesMammalian orthoreovirus 1 Lang
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.35 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 1.4Jun 19, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,41310
Polymers42,8913
Non-polymers5237
Water14,718817
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area15900 Å2
ΔGint-167 kcal/mol
Surface area20410 Å2
MethodPISA
Unit cell
Length a, b, c (Å)52.700, 37.590, 89.720
Angle α, β, γ (deg.)90.00, 100.53, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 14296.860 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mammalian orthoreovirus 1 Lang / Gene: S1 / Production host: Escherichia coli (E. coli) / References: UniProt: P04506
#2: Chemical ChemComp-IOD / IODIDE ION


Mass: 126.904 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: I
#3: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 817 / 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: 2.04 Å3/Da / Density % sol: 40.59 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 9.5 / Details: 18% (v/v) PEG8000, 0.1M CAPS pH 9.5, 0.2M NaI

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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 24, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.35→48.73 Å / Num. obs: 76273 / % possible obs: 99.9 % / Redundancy: 6.6 % / Biso Wilson estimate: 12.04 Å2 / CC1/2: 0.999 / Rrim(I) all: 0.109 / Net I/σ(I): 12
Reflection shellResolution: 1.35→1.39 Å / Redundancy: 6 % / Mean I/σ(I) obs: 1.9 / Num. unique obs: 5563 / CC1/2: 0.723 / Rrim(I) all: 0.876 / % possible all: 99.9

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Processing

Software
NameVersionClassification
BUSTER2.10.0refinement
XDSdata reduction
XDSdata scaling
autoSHARPphasing
RefinementMethod to determine structure: SAD / Resolution: 1.35→48.73 Å / Cor.coef. Fo:Fc: 0.9488 / Cor.coef. Fo:Fc free: 0.9443 / SU R Cruickshank DPI: 0.06 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.067 / SU Rfree Blow DPI: 0.067 / SU Rfree Cruickshank DPI: 0.062
RfactorNum. reflection% reflectionSelection details
Rfree0.2026 3831 5.02 %RANDOM
Rwork0.175 ---
obs0.1764 76268 99.93 %-
Displacement parametersBiso mean: 15.97 Å2
Baniso -1Baniso -2Baniso -3
1-3.5875 Å20 Å22.9976 Å2
2---1.3206 Å20 Å2
3----2.267 Å2
Refine analyzeLuzzati coordinate error obs: 0.148 Å
Refinement stepCycle: 1 / Resolution: 1.35→48.73 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3104 0 7 817 3928
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0153150HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.244347HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1242SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes101HARMONIC2
X-RAY DIFFRACTIONt_gen_planes507HARMONIC5
X-RAY DIFFRACTIONt_it3150HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion2.39
X-RAY DIFFRACTIONt_other_torsion14.61
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion494SEMIHARMONIC5
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_contact4849SEMIHARMONIC4
LS refinement shellResolution: 1.35→1.39 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2574 284 5.11 %
Rwork0.2168 5273 -
all0.2188 5557 -
obs--99.93 %

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