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- PDB-6fjq: Adenovirus species 48, fiber knob protein -

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Basic information

Entry
Database: PDB / ID: 6fjq
TitleAdenovirus species 48, fiber knob protein
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, 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 / Sandwich / Mainly Beta
Similarity search - Domain/homology
Biological speciesHuman adenovirus 48
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.91 Å
AuthorsRizkallah, P.J. / Parker, A.L. / Baker, A.T.
CitationJournal: Nat Commun / 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 1.1Mar 6, 2019Group: Data collection / Database references / Category: citation / citation_author / pdbx_database_proc
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Jan 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 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Fiber
B: Fiber
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,52612
Polymers43,6752
Non-polymers85110
Water1629
1
A: Fiber
hetero molecules

A: Fiber
hetero molecules

A: Fiber
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,55115
Polymers65,5123
Non-polymers1,03912
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_456z-1/2,-x+1/2,-y+11
crystal symmetry operation12_565-y+1/2,-z+1,x+1/21
Buried area8910 Å2
ΔGint-90 kcal/mol
Surface area24110 Å2
MethodPISA
2
B: Fiber
hetero molecules

B: Fiber
hetero molecules

B: Fiber
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,02621
Polymers65,5123
Non-polymers1,51318
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_456z-1/2,-x+1/2,-y+11
crystal symmetry operation12_565-y+1/2,-z+1,x+1/21
Buried area9700 Å2
ΔGint-149 kcal/mol
Surface area24000 Å2
MethodPISA
Unit cell
Length a, b, c (Å)145.205, 145.205, 145.205
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number212
Space group name H-MP4332
Components on special symmetry positions
IDModelComponents
11A-401-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: ASP / Beg label comp-ID: ASP / End auth comp-ID: GLU / End label comp-ID: GLU / Refine code: _ / Auth seq-ID: 2 - 196 / Label seq-ID: 1 - 195

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

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Components

#1: Protein Fiber


Mass: 21837.484 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human adenovirus 48 / Production host: Escherichia coli (E. coli) / References: UniProt: A4ZKK6
#2: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 9 / 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: 2.92 Å3/Da / Density % sol: 57.89 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: 0.1 M Bis-Tris-propane, 20% PEG 3350, 0.2M NaNO3

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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: 2.91→83.82 Å / Num. obs: 12061 / % possible obs: 100 % / Redundancy: 41.2 % / Biso Wilson estimate: 74.5 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.125 / Rrim(I) all: 0.127 / Net I/σ(I): 22.2
Reflection shellResolution: 2.91→2.99 Å / Redundancy: 41.4 % / Rmerge(I) obs: 3.026 / Num. unique obs: 877 / CC1/2: 0.705 / Rrim(I) all: 3.063 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0189refinement
xia2data reduction
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1KNB

1knb


Resolution: 2.91→83.83 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.853 / SU B: 45.861 / SU ML: 0.37 / Cross valid method: THROUGHOUT / ESU R Free: 0.453 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.29134 572 4.8 %RANDOM
Rwork0.20083 ---
obs0.20525 11371 99.4 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 84.911 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: 1 / Resolution: 2.91→83.83 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3076 0 49 9 3134
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.023191
X-RAY DIFFRACTIONr_bond_other_d0.0020.022845
X-RAY DIFFRACTIONr_angle_refined_deg2.2931.9724332
X-RAY DIFFRACTIONr_angle_other_deg1.21736683
X-RAY DIFFRACTIONr_dihedral_angle_1_deg10.2435388
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.85526.176136
X-RAY DIFFRACTIONr_dihedral_angle_3_deg21.37115534
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.44152
X-RAY DIFFRACTIONr_chiral_restr0.1380.2483
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0213476
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02598
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_it3.756.0851558
X-RAY DIFFRACTIONr_mcbond_other3.7496.0851557
X-RAY DIFFRACTIONr_mcangle_it5.9259.1241944
X-RAY DIFFRACTIONr_mcangle_other5.9239.1241945
X-RAY DIFFRACTIONr_scbond_it3.9476.2891633
X-RAY DIFFRACTIONr_scbond_other3.7056.2271613
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.8729.2592359
X-RAY DIFFRACTIONr_long_range_B_refined9.6869.4473385
X-RAY DIFFRACTIONr_long_range_B_other9.68169.4683386
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Number: 11828 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.11 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 2.911→2.986 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.57 46 -
Rwork0.389 800 -
obs--97.8 %
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)
10.41650.5493-0.27772.1684-0.20574.2314-0.0404-0.0572-0.28670.0734-0.0303-0.15880.41390.19130.07070.0780.04090.01180.02590.02930.24928.244425.569599.8336
20.51120.9051-0.53394.0457-0.43582.3495-0.13930.38170.139-0.70350.15670.2808-0.0349-0.399-0.01740.26670.0418-0.13260.41820.07450.09755.495258.604164.5231
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 196
2X-RAY DIFFRACTION2B2 - 196

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