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- PDB-6zc5: Human Adenovirus serotype D10 FiberKnob protein -

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Basic information

Entry
Database: PDB / ID: 6zc5
TitleHuman Adenovirus serotype D10 FiberKnob protein
ComponentsFiber
KeywordsVIRAL PROTEIN / Adenovirus / AdV / HAdV / HAdV-D10 / Ad10 / serotype 10 / Fiber / Fiber-knob / Fibre / knob domain / head / pIV / protein IV / Adenoviridae
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
Biological speciesHuman adenovirus D10
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.5 Å
AuthorsBaker, A.T. / Mundy, R.M. / Rizkallah, P.J. / Parker, A.L.
CitationJournal: Mol Ther Oncolytics / Year: 2022
Title: Development of a low-seroprevalence, alpha v beta 6 integrin-selective virotherapy based on human adenovirus type 10.
Authors: Bates, E.A. / Davies, J.A. / Vanova, J. / Nestic, D. / Meniel, V.S. / Koushyar, S. / Cunliffe, T.G. / Mundy, R.M. / Moses, E. / Uusi-Kerttula, H.K. / Baker, A.T. / Cole, D.K. / Majhen, D. / ...Authors: Bates, E.A. / Davies, J.A. / Vanova, J. / Nestic, D. / Meniel, V.S. / Koushyar, S. / Cunliffe, T.G. / Mundy, R.M. / Moses, E. / Uusi-Kerttula, H.K. / Baker, A.T. / Cole, D.K. / Majhen, D. / Rizkallah, P.J. / Phesse, T. / Chester, J.D. / Parker, A.L.
History
DepositionJun 9, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 30, 2021Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2022Group: Database references / Category: citation / citation_author / database_2
Item: _citation.journal_abbrev / _citation.journal_id_CSD ..._citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Jan 24, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / 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
B: Fiber
C: Fiber
D: Fiber
E: Fiber
F: Fiber
G: Fiber
H: Fiber
I: Fiber
J: Fiber
K: Fiber
L: Fiber


Theoretical massNumber of molelcules
Total (without water)256,02012
Polymers256,02012
Non-polymers00
Water0
1
A: Fiber
B: Fiber
C: Fiber


Theoretical massNumber of molelcules
Total (without water)64,0053
Polymers64,0053
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6050 Å2
ΔGint-28 kcal/mol
Surface area22760 Å2
MethodPISA
2
D: Fiber
E: Fiber
F: Fiber


Theoretical massNumber of molelcules
Total (without water)64,0053
Polymers64,0053
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6140 Å2
ΔGint-33 kcal/mol
Surface area22930 Å2
MethodPISA
3
G: Fiber
H: Fiber
I: Fiber


Theoretical massNumber of molelcules
Total (without water)64,0053
Polymers64,0053
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6150 Å2
ΔGint-32 kcal/mol
Surface area23020 Å2
MethodPISA
4
J: Fiber
K: Fiber
L: Fiber


Theoretical massNumber of molelcules
Total (without water)64,0053
Polymers64,0053
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5940 Å2
ΔGint-29 kcal/mol
Surface area22300 Å2
MethodPISA
Unit cell
Length a, b, c (Å)101.357, 101.357, 326.717
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number144
Space group name H-MP31

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Components

#1: Protein
Fiber / / Fiber protein


Mass: 21335.000 Da / Num. of mol.: 12
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human adenovirus D10 / Gene: L5 / Production host: Escherichia coli (E. coli) / References: UniProt: B5BQ05

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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: 3.78 Å3/Da / Density % sol: 67.5 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6 / Details: 0.2 M CaCl2, 0.1 MES, 20% w/v PEG 6000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.91587 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Oct 30, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91587 Å / Relative weight: 1
Reflection twin
Crystal-IDIDOperatorDomain-IDFraction
11H, K, L10.253
11K, H, -L20.254
11-h,-k,l30.245
11-K, -H, -L40.248
ReflectionResolution: 2.5→108.91 Å / Num. obs: 128287 / % possible obs: 98.7 % / Redundancy: 5.8 % / CC1/2: 0.996 / Rmerge(I) obs: 0.147 / Rpim(I) all: 0.067 / Rrim(I) all: 0.162 / Net I/σ(I): 6.7 / Num. measured all: 741038 / Scaling rejects: 3
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
2.5-2.5462.7663853064400.7321.2313.030.899.3
13.69-108.915.40.06943157970.9930.0330.07622.499.1

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation5.28 Å108.91 Å
Translation5.28 Å108.91 Å

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Processing

Software
NameVersionClassificationNB
XDSdata reduction
Aimless0.7.4data scaling
PHASER2.8.3phasing
REFMAC5.8.0258refinement
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6STT

6stt


Resolution: 2.5→108.91 Å / Cor.coef. Fo:Fc: 0.925 / Cor.coef. Fo:Fc free: 0.93 / SU B: 1.948 / SU ML: 0.05 / SU R Cruickshank DPI: 0.069 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.069 / ESU R Free: 0.052 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2512 6341 4.9 %RANDOM
Rwork0.219 ---
obs0.2206 121851 98.64 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 254.22 Å2 / Biso mean: 78.737 Å2 / Biso min: 3.65 Å2
Baniso -1Baniso -2Baniso -3
1-63.93 Å20 Å20 Å2
2--63.93 Å20 Å2
3----127.86 Å2
Refinement stepCycle: final / Resolution: 2.5→108.91 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms17536 0 0 0 17536
Num. residues----2211
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.01317950
X-RAY DIFFRACTIONr_bond_other_d0.0020.01716198
X-RAY DIFFRACTIONr_angle_refined_deg1.5761.65224408
X-RAY DIFFRACTIONr_angle_other_deg1.0961.57537847
X-RAY DIFFRACTIONr_dihedral_angle_1_deg10.00452199
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.80724.638815
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.951153036
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.681536
X-RAY DIFFRACTIONr_chiral_restr0.0690.22487
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0219867
X-RAY DIFFRACTIONr_gen_planes_other0.0020.023617
LS refinement shellResolution: 2.5→2.565 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.344 400 -
Rwork0.309 9152 -
all-9552 -
obs--98.85 %

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