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- PDB-3f0y: Crystal structure of the human Adenovirus type 14 fiber knob -

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Basic information

Entry
Database: PDB / ID: 3f0y
TitleCrystal structure of the human Adenovirus type 14 fiber knob
ComponentsFiber protein
KeywordsVIRAL PROTEIN / adenovirus / Ad14 / CD46 / trimer / fiber / knob
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
IMIDAZOLE / Fiber protein
Similarity search - Component
Biological speciesHuman adenovirus 14
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 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 27, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 25, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.2Dec 27, 2023Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_special_symmetry / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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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
G: Fiber protein
H: Fiber protein
I: Fiber protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)207,86916
Polymers207,2939
Non-polymers5767
Water32,4811803
1
A: Fiber protein
B: Fiber protein
C: Fiber protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,5819
Polymers69,0983
Non-polymers4846
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7170 Å2
ΔGint-26 kcal/mol
Surface area22090 Å2
MethodPISA
2
D: Fiber protein
E: Fiber protein
F: Fiber protein


Theoretical massNumber of molelcules
Total (without water)69,0983
Polymers69,0983
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6300 Å2
ΔGint-36 kcal/mol
Surface area22220 Å2
MethodPISA
3
G: Fiber protein
H: Fiber protein
I: Fiber protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,1904
Polymers69,0983
Non-polymers921
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6680 Å2
ΔGint-38 kcal/mol
Surface area22830 Å2
MethodPISA
Unit cell
Length a, b, c (Å)106.470, 106.470, 311.710
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number153
Space group name H-MP3212
Components on special symmetry positions
IDModelComponents
11B-1323-

HOH

21F-797-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11B
21A
12I
22A
/ NCS ensembles :
ID
1
2

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Components

#1: Protein
Fiber protein


Mass: 23032.607 Da / Num. of mol.: 9 / Fragment: resdiues 123-325
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human adenovirus 14 / Strain: De Wit / Gene: Fiber, L5 / Plasmid: pET15b / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta 2 (DE3) / References: UniProt: Q8V791
#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-IMD / IMIDAZOLE


Mass: 69.085 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H5N2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1803 / 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: 2.46 Å3/Da / Density % sol: 50.01 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 9
Details: 20% (w/v) PEG 8000, 0.1M CHES, 200mM NaCl, pH 9.0, VAPOR DIFFUSION, SITTING DROP, temperature 293.15K

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Data collection

DiffractionMean temperature: 93.15 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Nov 11, 2007
RadiationMonochromator: Undulator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.8→47.4 Å / Num. all: 187138 / Num. obs: 185386 / % possible obs: 99.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Rmerge(I) obs: 0.078
Reflection shellResolution: 1.8→1.9 Å / % possible all: 94.4

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Processing

Software
NameVersionClassification
MAR345dtbdata collection
PHASERphasing
REFMAC5.3.0037refinement
XDSdata reduction
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Human Adenovirus type 11 fiber knob

Resolution: 1.8→47.4 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.938 / SU B: 2.745 / SU ML: 0.085 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.129 / ESU R Free: 0.118 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21495 9272 5 %RANDOM
Rwork0.18803 ---
obs0.18937 176156 100 %-
all-176156 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 14.92 Å2
Baniso -1Baniso -2Baniso -3
1-0.03 Å20.01 Å20 Å2
2--0.03 Å20 Å2
3----0.04 Å2
Refinement stepCycle: LAST / Resolution: 1.8→47.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13904 0 39 1803 15746
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0040.02214416
X-RAY DIFFRACTIONr_bond_other_d0.0010.029131
X-RAY DIFFRACTIONr_angle_refined_deg0.9261.93119716
X-RAY DIFFRACTIONr_angle_other_deg0.748322375
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.92951826
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.41624.903667
X-RAY DIFFRACTIONr_dihedral_angle_3_deg9.937152246
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.8351555
X-RAY DIFFRACTIONr_chiral_restr0.0570.22283
X-RAY DIFFRACTIONr_gen_planes_refined0.0020.0216274
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022956
X-RAY DIFFRACTIONr_nbd_refined0.1670.22632
X-RAY DIFFRACTIONr_nbd_other0.1780.210634
X-RAY DIFFRACTIONr_nbtor_refined0.170.27347
X-RAY DIFFRACTIONr_nbtor_other0.0790.27544
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1180.21978
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1550.226
X-RAY DIFFRACTIONr_symmetry_vdw_other0.1630.295
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.080.246
X-RAY DIFFRACTIONr_mcbond_it0.4391.511588
X-RAY DIFFRACTIONr_mcbond_other0.0391.53602
X-RAY DIFFRACTIONr_mcangle_it0.485214656
X-RAY DIFFRACTIONr_scbond_it0.58436465
X-RAY DIFFRACTIONr_scangle_it0.864.55035
Refine LS restraints NCS

Dom-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Ens-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
1B127tight positional0.010.05
2I45medium positional0.240.5
1B127tight thermal0.040.5
2I45medium thermal0.092
LS refinement shellResolution: 1.8→1.848 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.286 637 -
Rwork0.25 12099 -
obs--100 %

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