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- PDB-6fjo: Adenovirus species 26 knob protein, very high resolution -

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Basic information

Entry
Database: PDB / ID: 6fjo
TitleAdenovirus species 26 knob protein, very high resolution
ComponentsFiber
KeywordsVIRAL PROTEIN / Fiber / Fiber-knob / tropism determinant / high resolution / structure determination. adenovirus / Mastadenovirus
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
Adenovirus pIV-related, attachment domain / Adenovirus Type 5 Fiber Protein (Receptor Binding Domain) / Adenoviral fibre protein, repeat/shaft region / Adenoviral fibre protein, knob / Adenoviral fibre protein (knob domain) / Adenoviral fibre protein (repeat/shaft region) / Adenovirus fibre protein / Attachment protein shaft domain superfamily / Adenovirus pIV-like, attachment domain / Sandwich / Mainly Beta
Similarity search - Domain/homology
GLUTAMIC ACID / Fiber
Similarity search - Component
Biological speciesHuman adenovirus 26
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.17 Å
AuthorsRizkallah, P.J. / Parker, A.L. / Baker, A.T.
Citation
Journal: Sci Adv / Year: 2019
Title: Human adenovirus type 26 uses sialic acid-bearing glycans as a primary cell entry receptor.
Authors: Baker, A.T. / Mundy, R.M. / Davies, J.A. / Rizkallah, P.J. / Parker, A.L.
#1: Journal: Biorxiv / Year: 2019
Title: Diversity within the adenovirus fiber knob hypervariable loops influences primary receptor interactions.
Authors: Baker, A.T. / Greenshields-Watson, A. / Coughlan, L. / Davies, J.A. / Uusi-Kerttula, H. / Cole, D.K. / Rizkallah, P.J. / Parker, A.L.
History
DepositionJan 22, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 6, 2019Provider: repository / Type: Initial release
Revision 1.1Feb 13, 2019Group: Data collection / Database references
Category: citation / citation_author ...citation / citation_author / pdbx_database_proc / pdbx_database_related
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.pdbx_database_id_DOI / _citation.title / _citation.year
Revision 1.2May 1, 2019Group: Data collection / Database references / Category: citation / pdbx_database_proc / Item: _citation.year
Revision 1.3Sep 18, 2019Group: Data collection / Database references / Category: citation / citation_author
Revision 1.4Sep 25, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 1.5Jan 17, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / pdbx_initial_refinement_model
Item: _citation.journal_id_ISSN / _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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,9834
Polymers20,6481
Non-polymers3353
Water3,081171
1
A: Fiber
hetero molecules

A: Fiber
hetero molecules

A: Fiber
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,95012
Polymers61,9453
Non-polymers1,0069
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555z,x,y1
crystal symmetry operation9_555y,z,x1
Buried area7570 Å2
ΔGint-57 kcal/mol
Surface area20640 Å2
MethodPISA
Unit cell
Length a, b, c (Å)85.776, 85.776, 85.776
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number198
Space group name H-MP213

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Components

#1: Protein Fiber


Mass: 20648.195 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human adenovirus 26 / Production host: Escherichia coli (E. coli) / References: UniProt: A4ZKM1
#2: Chemical ChemComp-GLU / GLUTAMIC ACID


Type: L-peptide linking / Mass: 147.129 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H9NO4
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 171 / 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: 2.55 Å3/Da / Density % sol: 51.71 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4 / Details: PACT premier A01: 0.1 M SPG buffer, 25% PEG 1500

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: May 12, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.17→85.78 Å / Num. obs: 71878 / % possible obs: 100 % / Redundancy: 21.8 % / Biso Wilson estimate: 12.2 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.065 / Rrim(I) all: 0.066 / Net I/σ(I): 24.8
Reflection shellResolution: 1.17→1.23 Å / Redundancy: 21.2 % / Rmerge(I) obs: 1.37 / Mean I/σ(I) obs: 2.3 / Num. unique obs: 10438 / CC1/2: 0.825 / Rrim(I) all: 1.404 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
xia2data reduction
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1KNB

1knb


Resolution: 1.17→60.65 Å / Cor.coef. Fo:Fc: 0.973 / Cor.coef. Fo:Fc free: 0.967 / SU B: 1.185 / SU ML: 0.026 / Cross valid method: THROUGHOUT / ESU R: 0.034 / ESU R Free: 0.036 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19018 3558 5 %RANDOM
Rwork0.16886 ---
obs0.16992 68283 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 19.89 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: 1 / Resolution: 1.17→60.65 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1452 0 21 171 1644
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0210.021635
X-RAY DIFFRACTIONr_bond_other_d0.0020.021453
X-RAY DIFFRACTIONr_angle_refined_deg2.081.9592246
X-RAY DIFFRACTIONr_angle_other_deg1.09633412
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.1015211
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.54225.29468
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.27915280
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.297154
X-RAY DIFFRACTIONr_chiral_restr0.1220.2256
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.0211859
X-RAY DIFFRACTIONr_gen_planes_other0.0040.02325
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_it1.1491.157808
X-RAY DIFFRACTIONr_mcbond_other1.1471.155807
X-RAY DIFFRACTIONr_mcangle_it1.9811.7331031
X-RAY DIFFRACTIONr_mcangle_other1.9821.7371032
X-RAY DIFFRACTIONr_scbond_it1.4531.334827
X-RAY DIFFRACTIONr_scbond_other1.451.334827
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.2081.9361216
X-RAY DIFFRACTIONr_long_range_B_refined5.65415.2721870
X-RAY DIFFRACTIONr_long_range_B_other5.51614.6941837
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.165→1.195 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.243 264 -
Rwork0.24 4997 -
obs--100 %
Refinement TLS params.Method: refined / Origin x: 2.2697 Å / Origin y: -1.272 Å / Origin z: 19.3226 Å
111213212223313233
T0.0213 Å2-0.0063 Å20.014 Å2-0.0144 Å20.0052 Å2--0.0171 Å2
L0.7594 °2-0.1493 °2-0.3384 °2-2.5097 °20.35 °2--1.2125 °2
S-0.0649 Å °-0.0049 Å °-0.0822 Å °0.0957 Å °0.0274 Å °0.107 Å °0.1306 Å °-0.1092 Å °0.0375 Å °

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