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- PDB-5n8d: Structure of the distal domain of mouse adenovirus 2 fibre, P21 native -

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Basic information

Entry
Database: PDB / ID: 5n8d
TitleStructure of the distal domain of mouse adenovirus 2 fibre, P21 native
ComponentsFiber
KeywordsVIRAL PROTEIN / Triple beta-spiral / 3-bladed propeller / ABCJ-GHID topology / N-acetyl-glucosamine binding
Function / homology
Function and homology information


adhesion receptor-mediated virion attachment to host cell / viral capsid / cell adhesion / symbiont entry into host cell / host cell nucleus
Similarity search - Function
Adenoviral fibre protein, repeat/shaft region / Adenoviral fibre protein (repeat/shaft region) / Adenovirus fibre protein / Attachment protein shaft domain superfamily
Similarity search - Domain/homology
Biological speciesMurine adenovirus 2
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsSingh, A.K. / van Raaij, M.J.
Funding support Spain, 4items
OrganizationGrant numberCountry
Spanish Ministry of Economy and CompetitivenessBFU2011-24843 Spain
Spanish Ministry of Economy and CompetitivenessBFU2014-53425-P Spain
Spanish Ministry of Economy and CompetitivenessBIO2015-68990-REDT Spain
Spanish Ministry of Economy and CompetitivenessFIS2011-16090-E Spain
CitationJournal: J. Gen. Virol. / Year: 2018
Title: Structure and N-acetylglucosamine binding of the distal domain of mouse adenovirus 2 fibre.
Authors: Singh, A.K. / Nguyen, T.H. / Vidovszky, M.Z. / Harrach, B. / Benko, M. / Kirwan, A. / Joshi, L. / Kilcoyne, M. / Berbis, M.A. / Canada, F.J. / Jimenez-Barbero, J. / Menendez, M. / Wilson, S. ...Authors: Singh, A.K. / Nguyen, T.H. / Vidovszky, M.Z. / Harrach, B. / Benko, M. / Kirwan, A. / Joshi, L. / Kilcoyne, M. / Berbis, M.A. / Canada, F.J. / Jimenez-Barbero, J. / Menendez, M. / Wilson, S.S. / Bromme, B.A. / Smith, J.G. / van Raaij, M.J.
History
DepositionFeb 23, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 14, 2018Provider: repository / Type: Initial release
Revision 1.1Oct 10, 2018Group: Data collection / Database references / Structure summary
Category: citation / citation_author / entity
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.name / _entity.formula_weight
Revision 1.2Nov 14, 2018Group: Data collection / Database references / Structure summary
Category: citation / entity
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _entity.formula_weight
Revision 1.3Jan 17, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
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: Fiber
B: Fiber
C: Fiber
D: Fiber
E: Fiber
F: Fiber
hetero molecules


Theoretical massNumber of molelcules
Total (without water)155,79421
Polymers154,8666
Non-polymers92815
Water29,9771664
1
A: Fiber
B: Fiber
C: Fiber
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,94311
Polymers77,4333
Non-polymers5108
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12680 Å2
ΔGint-128 kcal/mol
Surface area21640 Å2
MethodPISA
2
D: Fiber
E: Fiber
F: Fiber
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,85110
Polymers77,4333
Non-polymers4187
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12420 Å2
ΔGint-127 kcal/mol
Surface area21630 Å2
MethodPISA
Unit cell
Length a, b, c (Å)93.880, 100.600, 95.470
Angle α, β, γ (deg.)90.00, 116.28, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Fiber


Mass: 25810.922 Da / Num. of mol.: 6 / Fragment: UNP residues 587-787
Source method: isolated from a genetically manipulated source
Details: GSSHHHHHHSSGLVPRGSHMASMTGGQQMGRGSEF was an expression and purification tag, invisible in the electron density. The N-terminal residues GALTAQGA of the protein also did not show density.
Source: (gene. exp.) Murine adenovirus 2 / Plasmid: pET28a / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: E7CH51
#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1664 / 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: 2.61 Å3/Da / Density % sol: 52.88 % / Description: Plate
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 10 mM Tris-HCl, 4.0 M ammonium formate, 0.1 M HEPES-NaOH

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 1.0023 Å
DetectorType: Dectris / Detector: PIXEL / Date: Jan 31, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0023 Å / Relative weight: 1
ReflectionResolution: 1.8→29.66 Å / Num. obs: 144435 / % possible obs: 98.2 % / Redundancy: 2.8 % / Biso Wilson estimate: 16.5 Å2 / CC1/2: 0.989 / Rmerge(I) obs: 0.078 / Net I/σ(I): 7.1
Reflection shellResolution: 1.8→1.83 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.334 / Mean I/σ(I) obs: 2.1 / Num. unique obs: 7096 / CC1/2: 0.857 / % possible all: 97.8

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
Aimlessdata scaling
Cootmodel building
REFMAC5.8.0158refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5N83

5n83


Resolution: 1.8→29.66 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.942 / SU B: 2.643 / SU ML: 0.08 / Cross valid method: THROUGHOUT / ESU R: 0.103 / ESU R Free: 0.102 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20082 3644 2.5 %THIN SHELLS
Rwork0.16803 ---
obs0.16889 140696 98.09 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 24.019 Å2
Baniso -1Baniso -2Baniso -3
1--1.23 Å20 Å20.44 Å2
2---0.19 Å20 Å2
3---0.66 Å2
Refinement stepCycle: 1 / Resolution: 1.8→29.66 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9040 0 50 1664 10754
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.029467
X-RAY DIFFRACTIONr_bond_other_d0.0020.028478
X-RAY DIFFRACTIONr_angle_refined_deg1.5881.95812861
X-RAY DIFFRACTIONr_angle_other_deg0.887319742
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.75251176
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.29423.775408
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.997151549
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.8711549
X-RAY DIFFRACTIONr_chiral_restr0.0920.21466
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.02110502
X-RAY DIFFRACTIONr_gen_planes_other0.0020.022015
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_it1.8092.1824683
X-RAY DIFFRACTIONr_mcbond_other1.8082.1824682
X-RAY DIFFRACTIONr_mcangle_it2.8843.265851
X-RAY DIFFRACTIONr_mcangle_other2.8843.265852
X-RAY DIFFRACTIONr_scbond_it2.4062.4924784
X-RAY DIFFRACTIONr_scbond_other2.4052.4924784
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.863.637006
X-RAY DIFFRACTIONr_long_range_B_refined6.58328.56310748
X-RAY DIFFRACTIONr_long_range_B_other6.24727.33910270
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.8→1.897 Å / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.253 499 -
Rwork0.232 20353 -
obs--97.8 %

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