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- PDB-3exv: Crystal structure of the human Adenovirus type 11 fiber knob -

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Basic information

Entry
Database: PDB / ID: 3exv
TitleCrystal structure of the human Adenovirus type 11 fiber knob
ComponentsFiber protein
KeywordsVIRAL PROTEIN / adenovirus / fiber knob / attachment protein / trimer / CD46 / MCP / Ad11 / Fiber protein
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 B
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.45 Å
AuthorsPersson, B.D. / Reiter, D.M. / Arnberg, N. / Stehle, T.
CitationJournal: J.Virol. / Year: 2009
Title: An arginine switch in the species B adenovirus knob determines high-affinity engagement of cellular receptor CD46
Authors: Persson, B.D. / Muller, S. / Reiter, D.M. / Schmitt, B.B. / Marttila, M. / Sumowski, C.V. / Schweizer, S. / Scheu, U. / Ochsenfeld, C. / Arnberg, N. / Stehle, T.
History
DepositionOct 17, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 25, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jan 24, 2018Group: Structure summary / Category: audit_author / Item: _audit_author.name
Revision 1.3Dec 27, 2023Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.4Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Fiber protein


Theoretical massNumber of molelcules
Total (without water)23,7521
Polymers23,7521
Non-polymers00
Water3,333185
1
A: Fiber protein

A: Fiber protein

A: Fiber protein


Theoretical massNumber of molelcules
Total (without water)71,2573
Polymers71,2573
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_555-z,x,-y1
crystal symmetry operation11_555y,-z,-x1
Buried area6570 Å2
ΔGint-35 kcal/mol
Surface area22360 Å2
MethodPISA
Unit cell
Length a, b, c (Å)100.597, 100.597, 100.597
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number197
Space group name H-MI23
Components on special symmetry positions
IDModelComponents
11A-347-

HOH

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Components

#1: Protein Fiber protein / pIV


Mass: 23752.438 Da / Num. of mol.: 1 / Fragment: residues 117-325
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human adenovirus B / Strain: Slobiski / Gene: PIV / Plasmid: pET15b / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta DE3 / References: UniProt: P35774
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 185 / 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: 1.79 Å3/Da / Density % sol: 31.12 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 18% w/v PEG6000, 0.1M HEPES buffer, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293.15K

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Data collection

DiffractionMean temperature: 93 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: May 10, 2006
RadiationMonochromator: Undulator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.45→71 Å / Num. all: 30079 / Num. obs: 28526 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 6 % / Biso Wilson estimate: 14.1 Å2 / Rsym value: 0.045
Reflection shellResolution: 1.45→1.5 Å / Redundancy: 5.4 % / Rsym value: 0.388 / % possible all: 100

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Processing

Software
NameVersionClassification
MAR345dtbdata collection
AMoREphasing
REFMAC5refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Human Adenovirus type 3 fiber knob

Resolution: 1.45→23.71 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.939 / SU B: 1.295 / SU ML: 0.052 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.081 / ESU R Free: 0.082 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2246 1525 5.1 %RANDOM
Rwork0.19204 ---
obs0.19365 28526 99.93 %-
all-30079 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 9.959 Å2
Refinement stepCycle: LAST / Resolution: 1.45→23.71 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1579 0 0 185 1764
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.0221619
X-RAY DIFFRACTIONr_bond_other_d0.0020.021039
X-RAY DIFFRACTIONr_angle_refined_deg0.9181.9322221
X-RAY DIFFRACTIONr_angle_other_deg0.67932550
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.3915208
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.10624.73776
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.70515261
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.861158
X-RAY DIFFRACTIONr_chiral_restr0.0590.2260
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.021832
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02333
X-RAY DIFFRACTIONr_nbd_refined0.1840.2285
X-RAY DIFFRACTIONr_nbd_other0.1920.21157
X-RAY DIFFRACTIONr_nbtor_refined0.1740.2814
X-RAY DIFFRACTIONr_nbtor_other0.080.2847
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.0880.2164
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1080.222
X-RAY DIFFRACTIONr_symmetry_vdw_other0.210.256
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0730.229
X-RAY DIFFRACTIONr_mcbond_it0.551.51299
X-RAY DIFFRACTIONr_mcbond_other0.0541.5402
X-RAY DIFFRACTIONr_mcangle_it0.61521649
X-RAY DIFFRACTIONr_scbond_it0.7653730
X-RAY DIFFRACTIONr_scangle_it1.0964.5565
LS refinement shellResolution: 1.45→1.488 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.311 112 -
Rwork0.275 2072 -
obs--99.95 %

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