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- PDB-3cnc: Crystal Structure of Ad16 fiber knob -

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Basic information

Entry
Database: PDB / ID: 3cnc
TitleCrystal Structure of Ad16 fiber knob
ComponentsFiber protein
KeywordsVIRAL PROTEIN / adenovirus 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, repeat/shaft region / Adenoviral fibre protein, knob / Adenoviral fibre protein (knob domain) / 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 16
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsPache, L. / Venkataraman, S. / Nemerow, G.R. / Reddy, V.S.
CitationJournal: J.Virol. / Year: 2008
Title: Structural variations in species B adenovirus fibers impact CD46 association
Authors: Pache, L. / Venkataraman, S. / Reddy, V.S. / Nemerow, G.R.
History
DepositionMar 25, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 17, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 21, 2024Group: 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 1.3Apr 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
B: Fiber protein
C: Fiber protein
D: Fiber protein
E: Fiber protein
F: Fiber protein


Theoretical massNumber of molelcules
Total (without water)144,6906
Polymers144,6906
Non-polymers00
Water1,802100
1
A: Fiber protein
B: Fiber protein
C: Fiber protein


Theoretical massNumber of molelcules
Total (without water)72,3453
Polymers72,3453
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6030 Å2
ΔGint-27 kcal/mol
Surface area23550 Å2
MethodPISA
2
D: Fiber protein
E: Fiber protein
F: Fiber protein


Theoretical massNumber of molelcules
Total (without water)72,3453
Polymers72,3453
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6040 Å2
ΔGint-26.9 kcal/mol
Surface area23590 Å2
MethodPISA
Unit cell
Length a, b, c (Å)167.830, 167.830, 262.161
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522

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Components

#1: Protein
Fiber protein / Serotype 16 fiber


Mass: 24114.951 Da / Num. of mol.: 6 / Fragment: residues 151-353
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human adenovirus 16 / Gene: L5 / Plasmid: pET28a(+) / Production host: Escherichia coli (E. coli) / References: UniProt: Q67711
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 100 / 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: 3.68 Å3/Da / Density % sol: 66.6 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 100mM HEPES, pH 7.5, 0.7M NaH2PO4 and 0.85M KH2PO4, VAPOR DIFFUSION, HANGING DROP, 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 0.9793 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Aug 15, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2.4→50 Å / Num. obs: 85182 / Biso Wilson estimate: 51.2 Å2 / Rmerge(I) obs: 0.112 / Net I/σ(I): 45.4
Reflection shellResolution: 2.4→2.5 Å / Rmerge(I) obs: 0.881 / Mean I/σ(I) obs: 2

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Processing

Software
NameVersionClassification
CNS1.2refinement
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Ad11 fiber knob

Resolution: 2.4→49.32 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 100884934.74 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber / Details: BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.272 4323 5.1 %RANDOM
Rwork0.245 ---
obs0.245 85182 99.7 %-
all-85182 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 50.3183 Å2 / ksol: 0.35 e/Å3
Displacement parametersBiso mean: 65.3 Å2
Baniso -1Baniso -2Baniso -3
1-3.51 Å20 Å20 Å2
2--3.51 Å20 Å2
3----7.02 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.46 Å0.4 Å
Luzzati d res low-5 Å
Luzzati sigma a0.49 Å0.44 Å
Refinement stepCycle: LAST / Resolution: 2.4→49.32 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9168 0 0 100 9268
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.5
X-RAY DIFFRACTIONc_dihedral_angle_d27.5
X-RAY DIFFRACTIONc_improper_angle_d0.88
LS refinement shellResolution: 2.4→2.55 Å / Rfactor Rfree error: 0.014 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.377 684 4.9 %
Rwork0.357 13211 -
obs--99.2 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water.paramwater.top

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