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- PDB-2oj6: Crystal Structure of Reovirus T3D Attachment Protein Sigma1 head ... -

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Basic information

Entry
Database: PDB / ID: 2oj6
TitleCrystal Structure of Reovirus T3D Attachment Protein Sigma1 head domain D345N mutant
ComponentsViral attachment protein sigma 1
KeywordsVIRAL PROTEIN / beta-barrel / beta-spiral repeat / aspartic acid cluster / greek key motif / trimer
Function / homology
Function and homology information


viral outer capsid / virion component / cell adhesion / symbiont entry into host cell / virion attachment to host cell
Similarity search - Function
Virus attachment protein , globular domain / Viral attachment sigma 1, reoviral / Reovirus viral attachment protein sigma 1 / Adenovirus Type 5 Fiber Protein (Receptor Binding Domain) / Attachment protein shaft domain superfamily / Adenovirus pIV-like, attachment domain / Sandwich / Mainly Beta
Similarity search - Domain/homology
Outer capsid protein sigma-1 / Viral attachment protein sigma 1
Similarity search - Component
Biological speciesReovirus sp.
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 Å
AuthorsStehle, T. / Kirchner, E. / Dermody, T.S.
CitationJournal: J.Biol.Chem. / Year: 2007
Title: The Reovirus Sigma1 Aspartic Acid Sandwich: A TRIMERIZATION MOTIF POISED FOR CONFORMATIONAL CHANGE.
Authors: Schelling, P. / Guglielmi, K.M. / Kirchner, E. / Paetzold, B. / Dermody, T.S. / Stehle, T.
History
DepositionJan 12, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 13, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 18, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.4Oct 20, 2021Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Aug 30, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.end_auth_comp_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Viral attachment protein sigma 1
B: Viral attachment protein sigma 1
C: Viral attachment protein sigma 1
D: Viral attachment protein sigma 1
E: Viral attachment protein sigma 1
F: Viral attachment protein sigma 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)107,5698
Polymers107,5206
Non-polymers492
Water17,168953
1
A: Viral attachment protein sigma 1
B: Viral attachment protein sigma 1
C: Viral attachment protein sigma 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,7844
Polymers53,7603
Non-polymers241
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6920 Å2
ΔGint-49 kcal/mol
Surface area18650 Å2
MethodPISA
2
D: Viral attachment protein sigma 1
E: Viral attachment protein sigma 1
F: Viral attachment protein sigma 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,7844
Polymers53,7603
Non-polymers241
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6740 Å2
ΔGint-40 kcal/mol
Surface area18460 Å2
MethodPISA
Unit cell
Length a, b, c (Å)84.020, 51.600, 108.860
Angle α, β, γ (deg.)90.00, 95.59, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D
51E
61F

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: GLY / Beg label comp-ID: GLY / End auth comp-ID: TYR / End label comp-ID: TYR / Refine code: 3 / Auth seq-ID: 305 - 450 / Label seq-ID: 15 - 160

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB
3CC
4DD
5EE
6FF
Detailstwo copies of biological assembly (trimer) are present in the asymmetric unit

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Components

#1: Protein
Viral attachment protein sigma 1


Mass: 17920.049 Da / Num. of mol.: 6 / Fragment: head domain / Mutation: D345N
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Reovirus sp. / Gene: S1 / Plasmid: pGEX-4T-3 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3)pLysS / References: UniProt: Q86337, UniProt: P03528*PLUS
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 953 / 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: 2.2 Å3/Da / Density % sol: 44.11 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.9
Details: 0.1 M sodium cacodylate, 0.2 M magnesium sulfate, 20% PEG 8000; protein concentration 8 mg/ml, pH 6.9, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å
DetectorType: MAR CCD 225 mm / Detector: CCD / Date: Oct 19, 2006 / Details: undulator
RadiationMonochromator: LN2 cooled fixed-exit Si(111) monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.85→30 Å / Num. all: 79724 / Num. obs: 78687 / % possible obs: 98.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 4.4 % / Biso Wilson estimate: 15.9 Å2 / Rmerge(I) obs: 0.096 / Rsym value: 9.6 / Net I/σ(I): 6.5
Reflection shellResolution: 1.85→1.92 Å / Redundancy: 4 % / Rmerge(I) obs: 0.416 / Mean I/σ(I) obs: 1.4 / Num. unique all: 7740 / Rsym value: 41.6 / % possible all: 97.9

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
MAR345CCDdata collection
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: residues 293-455 of 1KKE

1kke


Resolution: 1.85→30 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.926 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.162 / ESU R Free: 0.149 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22364 7920 10.1 %RANDOM
Rwork0.17521 ---
obs0.1801 78676 98.69 %-
all-79724 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 17.219 Å2
Baniso -1Baniso -2Baniso -3
1--0.39 Å20 Å20.1 Å2
2--0.61 Å20 Å2
3----0.2 Å2
Refinement stepCycle: LAST / Resolution: 1.85→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7550 0 2 953 8505
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0227784
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.2021.93510657
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.35951001
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.30423.628339
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.573151140
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.5641542
X-RAY DIFFRACTIONr_chiral_restr0.0970.21155
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.026080
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2060.23493
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3160.25255
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1670.2869
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined0.0660.22
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2720.278
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1880.249
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.8251.54853
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.53527861
X-RAY DIFFRACTIONr_scbond_it2.49632931
X-RAY DIFFRACTIONr_scangle_it3.6864.52780
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Dom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
1A567tight positional0.10.05
2B567tight positional0.090.05
3C567tight positional0.10.05
4D567tight positional0.10.05
5E567tight positional0.080.05
6F567tight positional0.090.05
1A502loose positional0.435
2B502loose positional0.485
3C502loose positional0.475
4D502loose positional0.535
5E502loose positional0.565
6F502loose positional0.565
1A567tight thermal0.320.5
2B567tight thermal0.320.5
3C567tight thermal0.330.5
4D567tight thermal0.30.5
5E567tight thermal0.30.5
6F567tight thermal0.350.5
1A502loose thermal2.3910
2B502loose thermal2.1710
3C502loose thermal2.5610
4D502loose thermal2.0910
5E502loose thermal2.1510
6F502loose thermal2.6310
LS refinement shellResolution: 1.85→1.92 Å / Total num. of bins used: 14
RfactorNum. reflection% reflection
Rfree0.273 827 -
Rwork0.23 7254 -
obs-8081 98 %

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