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- PDB-28nv: Human Adenovirus type C5 knob protein with the KO1 mutation and A... -

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Basic information

Entry
Database: PDB / ID: 28nv
TitleHuman Adenovirus type C5 knob protein with the KO1 mutation and A20 insertion
ComponentsFiber protein
KeywordsVIRAL PROTEIN / Adenovirus / C5 / Fiber Knob protein / KO1 mutation
Function / homology
Function and homology information


viral capsid, fiber / adhesion receptor-mediated virion attachment to host cell / cell adhesion / symbiont entry into host cell / host cell nucleus
Similarity search - Function
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
Similarity search - Domain/homology
Biological speciesHuman adenovirus 5
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.27 Å
AuthorsRizkallah, P.J. / Swift, E.A. / Parker, A.L.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Cancer Research UK United Kingdom
CitationJournal: To Be Published
Title: Human Adenovirus type C5 knob protein with the KO1 mutation and A20 insertion
Authors: Rizkallah, P.J. / Swift, E.A.
History
DepositionFeb 10, 2026Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 25, 2026Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Fiber protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,5514
Polymers22,3651
Non-polymers1863
Water3,423190
1
A: Fiber protein
hetero molecules

A: Fiber protein
hetero molecules

A: Fiber protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,65412
Polymers67,0953
Non-polymers5599
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_555z+1/2,-x+1/2,-y1
crystal symmetry operation12_554-y+1/2,-z,x-1/21
Buried area6480 Å2
ΔGint-14 kcal/mol
Surface area20160 Å2
Unit cell
Length a, b, c (Å)85.283, 85.283, 85.283
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number198
Space group name H-MP213
Components on special symmetry positions
IDModelComponents
11A-702-

HOH

21A-703-

HOH

31A-850-

HOH

41A-885-

HOH

51A-886-

HOH

61A-890-

HOH

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Components

#1: Protein Fiber protein / SPIKE / Protein IV


Mass: 22365.033 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human adenovirus 5 / Gene: L5 / Production host: Escherichia coli (E. coli) / References: UniProt: P11818
#2: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 190 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationN

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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: 2.31 Å3/Da / Density % sol: 46.78 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.2 M Sodium malonate dibasic monohydrate, 0.1 M Bis-Tris propane, 20 % w/v PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.97628 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 12, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97628 Å / Relative weight: 1
ReflectionResolution: 1.27→60.3 Å / Num. obs: 54652 / % possible obs: 100 % / Redundancy: 32.8 % / CC1/2: 1 / Rmerge(I) obs: 0.083 / Rpim(I) all: 0.014 / Rrim(I) all: 0.084 / Net I/σ(I): 22.9
Reflection shellResolution: 1.27→1.29 Å / Redundancy: 8.6 % / Rmerge(I) obs: 2.24 / Mean I/σ(I) obs: 0.4 / Num. unique obs: 2700 / CC1/2: 0.353 / Rpim(I) all: 0.789 / Rrim(I) all: 2.386 / % possible all: 99.2

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
DIALSdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.27→60.3 Å / Cor.coef. Fo:Fc: 0.979 / Cor.coef. Fo:Fc free: 0.969 / SU B: 1.616 / SU ML: 0.033 / Cross valid method: THROUGHOUT / ESU R: 0.038 / ESU R Free: 0.039 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.17112 2725 5 %RANDOM
Rwork0.15657 ---
obs0.1573 51794 99.83 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 17.784 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: 1 / Resolution: 1.27→60.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1360 0 12 190 1562
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0131468
X-RAY DIFFRACTIONr_bond_other_d0.0010.0151350
X-RAY DIFFRACTIONr_angle_refined_deg1.6341.6432009
X-RAY DIFFRACTIONr_angle_other_deg1.4731.5733122
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.1875190
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.00324.35562
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.76915231
X-RAY DIFFRACTIONr_dihedral_angle_4_deg7.805153
X-RAY DIFFRACTIONr_chiral_restr0.080.2203
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.021703
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02331
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_it0.8551.195742
X-RAY DIFFRACTIONr_mcbond_other0.8551.194741
X-RAY DIFFRACTIONr_mcangle_it1.4161.79938
X-RAY DIFFRACTIONr_mcangle_other1.4151.791939
X-RAY DIFFRACTIONr_scbond_it1.2051.334726
X-RAY DIFFRACTIONr_scbond_other1.2041.334727
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other1.8751.9361072
X-RAY DIFFRACTIONr_long_range_B_refined4.3415.2521641
X-RAY DIFFRACTIONr_long_range_B_other3.9514.4751600
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.27→1.303 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.376 201 -
Rwork0.352 3689 -
obs--97.71 %
Refinement TLS params.Method: refined / Origin x: 12.965 Å / Origin y: 8.056 Å / Origin z: -16.5655 Å
111213212223313233
T0.0055 Å2-0.0054 Å2-0.0075 Å2-0.0221 Å2-0.0063 Å2--0.0251 Å2
L0.9121 °20.1284 °2-0.5849 °2-0.5171 °2-0.1207 °2--1.8086 °2
S-0.0004 Å °0.1097 Å °-0.0587 Å °-0.0282 Å °0.0055 Å °0.0929 Å °0.0776 Å °-0.1815 Å °-0.0051 Å °

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