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- PDB-8ofu: Human adenovirus type 53 fiber-knob protein -

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Basic information

Entry
Database: PDB / ID: 8ofu
TitleHuman adenovirus type 53 fiber-knob protein
ComponentsFiber protein
KeywordsVIRAL PROTEIN / Adenovirus / Fiber knob / Ad25
Function / homology
Function and homology information


viral capsid / cell adhesion / symbiont entry into host cell / virion attachment to host cell / host cell nucleus
Similarity search - Function
Adenoviral fibre protein, knob / Adenoviral fibre protein (knob domain) / Adenovirus fibre protein / Attachment protein shaft domain superfamily / Adenovirus pIV-like, attachment domain
Similarity search - Domain/homology
DI(HYDROXYETHYL)ETHER / Fiber protein
Similarity search - Component
Biological speciesHuman adenovirus 53
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.61 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/N0137941/1 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
Revision 1.3Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Fiber protein
B: Fiber protein
C: Fiber protein
D: Fiber protein
E: Fiber protein
F: Fiber protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)129,83540
Polymers127,2666
Non-polymers2,56934
Water17,691982
1
A: Fiber protein
B: Fiber protein
C: Fiber protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,97521
Polymers63,6333
Non-polymers1,34118
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9180 Å2
ΔGint-55 kcal/mol
Surface area21900 Å2
2
D: Fiber protein
E: Fiber protein
F: Fiber protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,86019
Polymers63,6333
Non-polymers1,22716
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8930 Å2
ΔGint-63 kcal/mol
Surface area21570 Å2
Unit cell
Length a, b, c (Å)206.314, 60.526, 93.837
Angle α, β, γ (deg.)90.00, 91.80, 90.00
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
22
33
44
55
66
77
88
99
1010
1111
1212
1313
1414
1515

NCS ensembles :
ID
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15

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Components

#1: Protein
Fiber protein


Mass: 21211.078 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human adenovirus 53 / Gene: L5 / Production host: Escherichia coli (E. coli) / References: UniProt: E5RWD1
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: SO4
#3: Chemical...
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 22 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C4H10O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 982 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationY

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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: 2.3 Å3/Da / Density % sol: 46.54 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: 0.2 M potassium thiocyanate, 20 % w/v PEG 3350, pH unadjusted

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.91188 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Dec 14, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91188 Å / Relative weight: 1
ReflectionResolution: 1.606→70.489 Å / Num. obs: 150644 / % possible obs: 99.7 % / Redundancy: 3.7 % / Biso Wilson estimate: 20.6 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.099 / Rpim(I) all: 0.059 / Rrim(I) all: 0.116 / Net I/σ(I): 8.7
Reflection shellResolution: 1.606→1.633 Å / Redundancy: 3.5 % / Rmerge(I) obs: 1.569 / Mean I/σ(I) obs: 0.8 / Num. unique obs: 7529 / CC1/2: 0.334 / Rpim(I) all: 0.972 / Rrim(I) all: 1.853 / % possible all: 99.4

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
Aimlessdata scaling
xia2data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.61→68.42 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.956 / SU B: 5.476 / SU ML: 0.09 / Cross valid method: THROUGHOUT / ESU R: 0.098 / ESU R Free: 0.092 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21275 7463 5 %RANDOM
Rwork0.19125 ---
obs0.19231 142637 99.31 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 25.206 Å2
Baniso -1Baniso -2Baniso -3
1-0.52 Å2-0 Å20.21 Å2
2---1.28 Å2-0 Å2
3---0.75 Å2
Refinement stepCycle: 1 / Resolution: 1.61→68.42 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8832 0 158 982 9972
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0139238
X-RAY DIFFRACTIONr_bond_other_d0.0010.0158753
X-RAY DIFFRACTIONr_angle_refined_deg1.5621.65812499
X-RAY DIFFRACTIONr_angle_other_deg1.3681.57920190
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.77951124
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.75324.049410
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.504151579
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.2651525
X-RAY DIFFRACTIONr_chiral_restr0.0780.21255
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0211114
X-RAY DIFFRACTIONr_gen_planes_other0.0020.022120
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_it0.7891.0374487
X-RAY DIFFRACTIONr_mcbond_other0.7891.0374486
X-RAY DIFFRACTIONr_mcangle_it1.411.555614
X-RAY DIFFRACTIONr_mcangle_other1.411.5515615
X-RAY DIFFRACTIONr_scbond_it0.8771.1764751
X-RAY DIFFRACTIONr_scbond_other0.8771.1774752
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other1.2791.6876886
X-RAY DIFFRACTIONr_long_range_B_refined6.91114.43210968
X-RAY DIFFRACTIONr_long_range_B_other6.86713.39410656
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A59930.11
12B59930.11
21A61040.1
22C61040.1
31A62130.09
32D62130.09
41A59500.11
42E59500.11
51A60920.11
52F60920.11
61B60070.1
62C60070.1
71B60030.1
72D60030.1
81B62930.09
82E62930.09
91B59150.12
92F59150.12
101C60700.09
102D60700.09
111C59030.11
112E59030.11
121C60510.1
122F60510.1
131D59250.11
132E59250.11
141D60310.11
142F60310.11
151E59660.12
152F59660.12
LS refinement shellResolution: 1.61→1.647 Å
RfactorNum. reflection% reflection
Rfree0.351 531 -
Rwork0.349 10175 -
obs--96 %
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)
11.191-0.0199-0.49311.28490.40371.8489-0.00880.11510.1189-0.06480.0585-0.0656-0.09790.0625-0.04970.0979-0.02320.00520.13420.02320.0172-15.352-11.17630.628
21.4711-0.1467-0.27561.39350.04271.1327-0.0351-0.0629-0.0820.05530.019-0.02680.1969-0.02050.01610.1488-0.00970.00750.11730.01440.0071-25.176-31.65845.794
31.25210.36870.35672.7906-0.65271.895-0.05260.25990.078-0.21150.09470.25880.1073-0.1806-0.04210.131-0.0554-0.02740.26850.03830.0321-37.429-24.97622.516
41.0141-0.4735-0.47191.46160.8112.4483-0.0543-0.2286-0.0970.21490.0612-0.13150.13980.1504-0.0070.15780.02510.00140.17870.04140.0397-22.274-20.40880.769
51.18350.08530.22291.1985-0.06391.0186-0.00190.02660.1105-0.02270.01-0.0211-0.1674-0.0249-0.00810.12910.02650.02410.12470.01180.0156-27.1450.23563.614
61.4728-0.2151-0.36453.1723-0.69951.6243-0.0301-0.21120.01010.18420.04460.2056-0.0172-0.2632-0.01440.12010.04420.04030.24450.01340.0633-45.246-5.99282.835
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A183 - 366
2X-RAY DIFFRACTION2B180 - 366
3X-RAY DIFFRACTION3C183 - 366
4X-RAY DIFFRACTION4D183 - 366
5X-RAY DIFFRACTION5E180 - 366
6X-RAY DIFFRACTION6F183 - 366

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