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- PDB-8ofp: Human adenovirus type 24 fiber-knob protein -

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Basic information

Entry
Database: PDB / ID: 8ofp
TitleHuman adenovirus type 24 fiber-knob protein
ComponentsFiber
KeywordsVIRAL PROTEIN / Adenovirus / Fiber knob / Ad24
Function / homology
Function and homology information


adhesion receptor-mediated virion attachment to host cell / viral capsid / cell adhesion / symbiont entry into host cell
Similarity search - Function
Adenoviral fibre protein, knob / Adenoviral fibre protein (knob domain) / Adenoviral fibre protein, repeat/shaft region / Adenoviral fibre protein (repeat/shaft region) / Adenovirus fibre protein / Attachment protein shaft domain superfamily / Adenovirus pIV-like, attachment domain
Similarity search - Domain/homology
Biological speciesHuman adenovirus 24
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.1 Å
AuthorsRizkallah, P.J. / Parker, A.L. / Mundy, R.M. / Baker, A.T.
Funding support United Kingdom, 2items
OrganizationGrant numberCountry
Medical Research Council (MRC, United Kingdom)MR/N013941/1 United Kingdom
Wellcome Trust517732 United Kingdom
CitationJournal: Npj Viruses / Year: 2023
Title: Broad sialic acid usage amongst species D human adenovirus.
Authors: Mundy, R.M. / Baker, A.T. / Bates, E.A. / Cunliffe, T.G. / Teijeira-Crespo, A. / Moses, E. / Rizkallah, P.J. / Parker, A.L.
History
DepositionMar 16, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 20, 2023Provider: repository / Type: Initial release
Revision 1.1Oct 11, 2023Group: Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_id_CSD ..._citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_volume / _citation.page_first / _citation.title
Revision 1.2May 8, 2024Group: Database references / Category: citation
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ISSN / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title

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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


Theoretical massNumber of molelcules
Total (without water)132,7496
Polymers132,7496
Non-polymers00
Water0
1
A: Fiber
B: Fiber
C: Fiber


Theoretical massNumber of molelcules
Total (without water)66,3743
Polymers66,3743
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6440 Å2
ΔGint-35 kcal/mol
Surface area23480 Å2
2
D: Fiber
E: Fiber
F: Fiber


Theoretical massNumber of molelcules
Total (without water)66,3743
Polymers66,3743
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6430 Å2
ΔGint-36 kcal/mol
Surface area24380 Å2
Unit cell
Length a, b, c (Å)51.259, 99.619, 113.549
Angle α, β, γ (deg.)90.00, 100.26, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Fiber /


Mass: 22124.816 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human adenovirus 24 / Gene: L5 / Production host: Escherichia coli (E. coli) / References: UniProt: M0QUI2

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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: 2.15 Å3/Da / Density % sol: 42.76 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 5 / Details: 0.1 M MMT Buffer, 25% PEG 1500

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Oct 17, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.9→55.96 Å / Num. obs: 25128 / % possible obs: 100 % / Redundancy: 3.8 % / CC1/2: 0.973 / Rmerge(I) obs: 0.15 / Rpim(I) all: 0.089 / Rrim(I) all: 0.175 / Χ2: 0.94 / Net I/σ(I): 4.4 / Num. measured all: 96302
Reflection shellResolution: 2.9→2.98 Å / % possible obs: 100 % / Redundancy: 3.9 % / Rmerge(I) obs: 1.117 / Num. measured all: 7260 / Num. unique obs: 1852 / CC1/2: 0.652 / Rpim(I) all: 0.649 / Rrim(I) all: 1.296 / Χ2: 0.99 / Net I/σ(I) obs: 1

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
Aimlessdata scaling
xia2data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.1→55.87 Å / Cor.coef. Fo:Fc: 0.927 / Cor.coef. Fo:Fc free: 0.868 / SU B: 115.018 / SU ML: 0.849 / Cross valid method: THROUGHOUT / ESU R Free: 0.719 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.33672 1004 4.9 %RANDOM
Rwork0.234 ---
obs0.23903 19502 99.89 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 93.976 Å2
Baniso -1Baniso -2Baniso -3
1-2.54 Å20 Å20.46 Å2
2--0.9 Å20 Å2
3----3.39 Å2
Refinement stepCycle: 1 / Resolution: 3.1→55.87 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8946 0 0 0 8946
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0139137
X-RAY DIFFRACTIONr_bond_other_d0.0010.0178345
X-RAY DIFFRACTIONr_angle_refined_deg1.3711.65512418
X-RAY DIFFRACTIONr_angle_other_deg1.0531.57919542
X-RAY DIFFRACTIONr_dihedral_angle_1_deg12.09551117
X-RAY DIFFRACTIONr_dihedral_angle_2_deg41.24525.277415
X-RAY DIFFRACTIONr_dihedral_angle_3_deg22.964151602
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.8431518
X-RAY DIFFRACTIONr_chiral_restr0.050.21285
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.029979
X-RAY DIFFRACTIONr_gen_planes_other0.0030.021743
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_it1.2723.1234498
X-RAY DIFFRACTIONr_mcbond_other1.2723.1234497
X-RAY DIFFRACTIONr_mcangle_it2.1924.6815605
X-RAY DIFFRACTIONr_mcangle_other2.1924.6815606
X-RAY DIFFRACTIONr_scbond_it0.9083.1774639
X-RAY DIFFRACTIONr_scbond_other0.9073.1774637
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other1.6324.7476813
X-RAY DIFFRACTIONr_long_range_B_refined3.64436.38410150
X-RAY DIFFRACTIONr_long_range_B_other3.64436.38510151
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 3.1→3.18 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.437 75 -
Rwork0.393 1445 -
obs--99.93 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
14.5807-0.53290.16586.5769-1.21512.9980.0990.19660.2587-2.41190.0483-0.90220.12970.3316-0.14732.1513-0.12550.03270.0986-0.06190.295419.334219.33145.1352
23.00520.10252.01816.30910.79045.55840.2529-0.1697-0.4606-1.5080.3225-0.64950.5190.2508-0.57541.4494-0.0892-0.30450.0591-0.03350.431816.0353-4.833217.4733
33.10820.446-0.39679.1954-1.81224.41040.0773-0.4538-0.0429-0.48090.2653-0.0698-0.0873-0.0227-0.34260.6146-0.0851-0.23320.2008-0.08710.259613.749219.406930.4843
44.49380.3660.21866.51920.5094.8536-0.2328-0.09430.40480.2411-0.03230.8098-0.9116-0.2880.26511.1180.0094-0.36340.1957-0.17120.41982.030969.177647.2389
52.3659-0.25830.23655.60081.55177.8962-0.3024-0.42490.00410.25880.00580.47920.3097-0.17750.29660.6812-0.071-0.15440.17-0.00620.33533.367843.125740.6372
64.73810.2868-1.87597.41572.40955.1641-0.0840.22910.0929-1.6216-0.43931.0651-1.0554-0.78970.52331.5180.0281-0.65060.23730.03090.3526-2.470761.617521.8171
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|187-375}A187 - 375
2X-RAY DIFFRACTION2{ B|187-375}B187 - 375
3X-RAY DIFFRACTION3{ C|187-375}C187 - 375
4X-RAY DIFFRACTION4{ D|187-375}D187 - 375
5X-RAY DIFFRACTION5{ E|187-375}E187 - 375
6X-RAY DIFFRACTION6{ F|187-375}F187 - 375

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