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- PDB-5nbh: Structure of the distal domain of mouse adenovirus 2 fibre, P2121... -

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Basic information

Entry
Database: PDB / ID: 5nbh
TitleStructure of the distal domain of mouse adenovirus 2 fibre, P212121 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: 1.7 Å
AuthorsSingh, A.K. / van Raaij, M.J.
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
DepositionMar 1, 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,5254
Polymers77,4333
Non-polymers921
Water12,106672
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: native gel electrophoresis, Protein is trimeric on SDS-PAGE gels if sample is not boiled prior to electrophoresis
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11210 Å2
ΔGint-81 kcal/mol
Surface area22210 Å2
MethodPISA
Unit cell
Length a, b, c (Å)55.872, 91.110, 128.922
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Fiber


Mass: 25810.922 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
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.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 672 / 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: 2.12 Å3/Da / Density % sol: 41.95 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 10 mM Tris-HCl, 10 % (w/v) PEG 4000, 0.1 M HEPES-NaOH, 0.1 M magnesium chloride

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.9763 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 21, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 1.7→34.1 Å / Num. obs: 68912 / % possible obs: 94.3 % / Redundancy: 3.5 % / Biso Wilson estimate: 14.5 Å2 / CC1/2: 0.983 / Rmerge(I) obs: 0.116 / Net I/σ(I): 6.3
Reflection shellResolution: 1.7→1.74 Å / Redundancy: 1.9 % / Rmerge(I) obs: 0.233 / Mean I/σ(I) obs: 2.1 / Num. unique obs: 3722 / CC1/2: 0.857 / % possible all: 69.6

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
Cootmodel building
Aimlessdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5N8D

5n8d


Resolution: 1.7→34.05 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.93 / SU B: 2.497 / SU ML: 0.08 / Cross valid method: THROUGHOUT / ESU R: 0.105 / ESU R Free: 0.109 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21621 3559 5.2 %THIN SHELLS
Rwork0.17182 ---
obs0.17422 65280 94.09 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 19.75 Å2
Baniso -1Baniso -2Baniso -3
1--0.48 Å20 Å20 Å2
2--0.37 Å20 Å2
3---0.11 Å2
Refinement stepCycle: 1 / Resolution: 1.7→34.05 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4515 0 6 672 5193
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.024730
X-RAY DIFFRACTIONr_bond_other_d0.0020.024215
X-RAY DIFFRACTIONr_angle_refined_deg1.5091.9556445
X-RAY DIFFRACTIONr_angle_other_deg0.88939821
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6385605
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.25123.913207
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.51315769
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.5451524
X-RAY DIFFRACTIONr_chiral_restr0.0860.2730
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0215308
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021012
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_it1.6751.8222351
X-RAY DIFFRACTIONr_mcbond_other1.6731.8212350
X-RAY DIFFRACTIONr_mcangle_it2.8072.7172940
X-RAY DIFFRACTIONr_mcangle_other2.8082.7182941
X-RAY DIFFRACTIONr_scbond_it2.112.0662379
X-RAY DIFFRACTIONr_scbond_other2.1092.0662379
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.3223.0163493
X-RAY DIFFRACTIONr_long_range_B_refined6.0923.2975273
X-RAY DIFFRACTIONr_long_range_B_other5.80422.5145085
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.7→1.817 Å / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.266 540 -
Rwork0.257 9409 -
obs--76.19 %

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