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- PDB-8ofs: Human adenovirus type 30 fiber-knob protein complexed with sialic acid -

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Basic information

Entry
Database: PDB / ID: 8ofs
TitleHuman adenovirus type 30 fiber-knob protein complexed with sialic acid
ComponentsFiber
KeywordsVIRAL PROTEIN / Adenovirus / Fiber knob / Ad25
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, 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
N-acetyl-beta-neuraminic acid / Fiber
Similarity search - Component
Biological speciesHuman adenovirus 30
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.56 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

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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)67,8006
Polymers66,8723
Non-polymers9283
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: homology
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8640 Å2
ΔGint-33 kcal/mol
Surface area24510 Å2
Unit cell
Length a, b, c (Å)62.130, 62.490, 71.800
Angle α, β, γ (deg.)90.00, 93.85, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
22
33
/ NCS ensembles :
ID
1
2
3

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Components

#1: Protein Fiber


Mass: 22290.828 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human adenovirus 30 / Strain: 30 / Gene: L5 / Production host: Escherichia coli (E. coli) / References: UniProt: M0QTV3
#2: Sugar ChemComp-SLB / N-acetyl-beta-neuraminic acid / N-acetylneuraminic acid / sialic acid / O-sialic acid / 5-N-ACETYL-BETA-D-NEURAMINIC ACID / BETA-SIALIC ACID


Type: D-saccharide, beta linking / Mass: 309.270 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C11H19NO9 / Feature type: SUBJECT OF INVESTIGATION
IdentifierTypeProgram
DNeup5AcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-neuraminic acidCOMMON NAMEGMML 1.0
b-D-Neup5AcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
Neu5AcSNFG CARBOHYDRATE SYMBOLGMML 1.0
Has ligand of interestY

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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: 2.07 Å3/Da / Density % sol: 40.67 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 8 / Details: 0.1M MMT [Malic acid, MES, Tris], 25% w/v 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: May 18, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.56→62.49 Å / Num. obs: 17735 / % possible obs: 99 % / Redundancy: 3.7 % / Biso Wilson estimate: 74.3 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.057 / Rpim(I) all: 0.034 / Rrim(I) all: 0.066 / Χ2: 0.95 / Net I/σ(I): 10.5
Reflection shellResolution: 2.56→2.63 Å / % possible obs: 99.3 % / Redundancy: 3.8 % / Rmerge(I) obs: 0.972 / Num. measured all: 5020 / Num. unique obs: 1327 / CC1/2: 0.824 / Rpim(I) all: 0.57 / Rrim(I) all: 1.131 / Χ2: 0.87 / Net I/σ(I) obs: 1.1

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation5.74 Å48.52 Å

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
XDSdata reduction
Aimless0.7.4data scaling
PHASER2.8.3phasing
PDB_EXTRACT3.27data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.56→48.56 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.936 / SU B: 107.9 / SU ML: 0.768 / Cross valid method: THROUGHOUT / ESU R Free: 0.405 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.29189 933 5.3 %RANDOM
Rwork0.2286 ---
obs0.2319 16730 98.61 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 130.013 Å2
Baniso -1Baniso -2Baniso -3
1--8.09 Å2-0 Å27.46 Å2
2---2.61 Å2-0 Å2
3---9.6 Å2
Refinement stepCycle: 1 / Resolution: 2.56→48.56 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4638 0 63 0 4701
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0134806
X-RAY DIFFRACTIONr_bond_other_d0.0010.0164447
X-RAY DIFFRACTIONr_angle_refined_deg1.2221.6526545
X-RAY DIFFRACTIONr_angle_other_deg1.061.58810342
X-RAY DIFFRACTIONr_dihedral_angle_1_deg9.455598
X-RAY DIFFRACTIONr_dihedral_angle_2_deg42.33226.567201
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.67115799
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0410.2661
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.025425
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021003
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_it3.0746.7412401
X-RAY DIFFRACTIONr_mcbond_other3.0746.742400
X-RAY DIFFRACTIONr_mcangle_it510.1062996
X-RAY DIFFRACTIONr_mcangle_other4.99910.1062997
X-RAY DIFFRACTIONr_scbond_it2.5776.8422405
X-RAY DIFFRACTIONr_scbond_other2.5776.8422406
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.41110.1863550
X-RAY DIFFRACTIONr_long_range_B_refined7.34977.6115080
X-RAY DIFFRACTIONr_long_range_B_other7.34877.615081
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 / Rms dev position: 0.12 Å / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumber
11A5783
12B5783
21A5746
22C5746
31B5783
32C5783
LS refinement shellResolution: 2.56→2.627 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.532 83 -
Rwork0.512 1199 -
obs--95.96 %
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)
15.3041-0.0488-1.54487.3979-2.38596.2044-0.00941.6601-0.1527-0.93540.1118-0.02360.7206-0.4918-0.10240.5475-0.02310.28150.5395-0.13540.601722.983-19.2437.353
28.3017-0.3878-0.98034.7776-1.44825.30870.2526-0.12671.42710.26980.18310.4161-0.5158-0.5111-0.43570.42180.03850.34640.0626-0.0520.902920.3941.93623.919
36.3067-0.66081.77774.1231-0.17197.4716-0.06030.5929-0.2931-0.26050.02820.86550.6575-1.3540.03210.2903-0.17970.3210.4176-0.07931.04821.671-17.56823.861
458.4853-58.3596-39.985458.236239.898627.33781.00471.7998-1.2128-0.9903-1.83461.2075-0.692-1.21350.82990.578-0.16470.42420.76210.09760.83328.616-20.51926.108
5204.3586339.9775.1548652.074971.388360.91051.9972-4.29398.99097.7293-13.05512.7769-2.00142.0511.05791.10420.29640.53371.21340.61296.3223.169-15.18334.433
66.598818.733914.6953108.7794-6.744975.0535-0.44960.580.5439-1.59562.30384.936-0.48730.7048-1.85420.8113-0.2845-0.16480.662-0.00951.063719.434-24.78730.002
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A183 - 382
2X-RAY DIFFRACTION2B183 - 383
3X-RAY DIFFRACTION3C183 - 382
4X-RAY DIFFRACTION4B401
5X-RAY DIFFRACTION5C401
6X-RAY DIFFRACTION6A401

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