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- PDB-9tab: Crystal Structure of Human Adenovirus 52 Short Fiber Knob Mutant ... -

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Basic information

Entry
Database: PDB / ID: 9tab
TitleCrystal Structure of Human Adenovirus 52 Short Fiber Knob Mutant N243R in Complex with alpha-(2,8)-Pentasialic Acid (DP5)
ComponentsFiber-1
KeywordsVIRAL PROTEIN / human 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
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
N-acetyl-alpha-neuraminic acid / Fiber-1
Similarity search - Component
Biological specieshuman adenovirus 52
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsVonmetz, K. / Stehle, T.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research Foundation (DFG)FOR2953 Germany
CitationJournal: To Be Published
Title: Crystal Structures of Human Adenovirus 52 Short Fiber Knob Mutants in Complex with alpha-(2,8)-Pentasialic Acid (DP5)
Authors: Vonmetz, K. / Stehle, T.
History
DepositionNov 18, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 26, 2026Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Fiber-1
B: Fiber-1
C: Fiber-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,8195
Polymers67,3923
Non-polymers4272
Water7,494416
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6920 Å2
ΔGint-56 kcal/mol
Surface area18670 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.446, 82.268, 93.421
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

#1: Protein Fiber-1


Mass: 22463.965 Da / Num. of mol.: 3 / Mutation: N243R
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) human adenovirus 52 / Production host: Escherichia coli (E. coli) / References: UniProt: A0MK70
#2: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#3: Sugar ChemComp-SIA / N-acetyl-alpha-neuraminic acid / N-acetylneuraminic acid / sialic acid / alpha-sialic acid / O-SIALIC ACID


Type: D-saccharide, alpha linking / Mass: 309.270 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H19NO9 / Feature type: SUBJECT OF INVESTIGATION
IdentifierTypeProgram
DNeup5AcaCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-a-D-neuraminic acidCOMMON NAMEGMML 1.0
a-D-Neup5AcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
Neu5AcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 416 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
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: 1.81 Å3/Da / Density % sol: 32.24 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 12.5 % (v/v) MPD; 12.5 % (w/v) PEG3350; 17.5 % (w/v) PEG1000, 0.1 M Tris/Bicine pH 8.5, 1.6 mM of each Glycine, Na L-Glutamate, DL-Alanine, DL-Lysine, DL-Serine

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 0.999995 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Feb 7, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.999995 Å / Relative weight: 1
ReflectionResolution: 1.9→44.25 Å / Num. obs: 38759 / % possible obs: 98.6 % / Redundancy: 3.52 % / Biso Wilson estimate: 14.71 Å2 / CC1/2: 0.993 / Rrim(I) all: 0.122 / Net I/σ(I): 9.52
Reflection shellResolution: 1.9→2.01 Å / Redundancy: 2.71 % / Mean I/σ(I) obs: 2.73 / Num. unique obs: 5951 / CC1/2: 0.836 / Rrim(I) all: 0.434 / % possible all: 95.2

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Processing

Software
NameVersionClassification
PHENIX1.16_3549refinement
PHENIX1.16_3549refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.9→44.25 Å / SU ML: 0.1881 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 19.0639
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2014 1937 5 %
Rwork0.1634 36805 -
obs0.1653 38742 98.61 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 17.24 Å2
Refinement stepCycle: LAST / Resolution: 1.9→44.25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3847 0 29 416 4292
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01034089
X-RAY DIFFRACTIONf_angle_d1.24535619
X-RAY DIFFRACTIONf_chiral_restr0.0823663
X-RAY DIFFRACTIONf_plane_restr0.007719
X-RAY DIFFRACTIONf_dihedral_angle_d19.35161442
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9-1.950.27161250.22552374X-RAY DIFFRACTION90.09
1.95-20.23981370.19092603X-RAY DIFFRACTION99.2
2-2.060.21431360.17132600X-RAY DIFFRACTION99.2
2.06-2.120.21311390.16452642X-RAY DIFFRACTION99.86
2.12-2.20.22371370.15572598X-RAY DIFFRACTION99.74
2.2-2.290.21011390.16222638X-RAY DIFFRACTION99.57
2.29-2.390.21581380.16572621X-RAY DIFFRACTION99.57
2.39-2.520.22651390.16682645X-RAY DIFFRACTION99.68
2.52-2.680.18571400.17192646X-RAY DIFFRACTION99.54
2.68-2.880.2311390.17472649X-RAY DIFFRACTION99.46
2.88-3.170.20271390.16912662X-RAY DIFFRACTION99.22
3.17-3.630.17791390.15292627X-RAY DIFFRACTION98.19
3.63-4.580.1721410.13922684X-RAY DIFFRACTION98.47
4.58-44.250.1751490.1592816X-RAY DIFFRACTION98.7

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