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

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Basic information

Entry
Database: PDB / ID: 9taa
TitleCrystal Structure of Human Adenovirus 52 Short Fiber Knob Mutant Q320R 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: 1.91 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)68,1328
Polymers67,3503
Non-polymers7825
Water3,963220
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7790 Å2
ΔGint-82 kcal/mol
Surface area18030 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.294, 81.645, 93.176
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: 22449.939 Da / Num. of mol.: 3 / Mutation: Q320R
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.: 4 / 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.: 220 / 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: 1.82 Å3/Da / Density % sol: 32.44 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion / pH: 8.65
Details: 12.5 % (v/v) MPD, 12.5 % (w/v) PEG3350 25 % (w/v) PEG1000, 0.1 M Tris/Bicine pH 8.65 ,1.6 mM of each Glycine, Na L-Glutamate, DL-Alanine, DL-Lysine, DL-Serine, Seed stock N243R 1:100

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.999998 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Oct 24, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.999998 Å / Relative weight: 1
ReflectionResolution: 1.91→46.59 Å / Num. obs: 38731 / % possible obs: 99.9 % / Redundancy: 6.75 % / Biso Wilson estimate: 27.04 Å2 / CC1/2: 0.997 / Rrim(I) all: 0.143 / Net I/σ(I): 10.47
Reflection shellResolution: 1.91→2.01 Å / Redundancy: 6.06 % / Mean I/σ(I) obs: 1.53 / Num. unique obs: 6133 / CC1/2: 0.64 / Rrim(I) all: 1.124 / % possible all: 99.3

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
PHENIX1.19.2_4158refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.91→46.59 Å / SU ML: 0.2105 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 19.3673
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.197 1937 5 %
Rwork0.1693 36788 -
obs0.1707 38725 99.84 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 30.55 Å2
Refinement stepCycle: LAST / Resolution: 1.91→46.59 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3781 0 53 220 4054
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00693946
X-RAY DIFFRACTIONf_angle_d0.94575405
X-RAY DIFFRACTIONf_chiral_restr0.0535638
X-RAY DIFFRACTIONf_plane_restr0.0086684
X-RAY DIFFRACTIONf_dihedral_angle_d14.13241361
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.91-1.960.32781350.29712560X-RAY DIFFRACTION98.5
1.96-2.010.29321360.2282578X-RAY DIFFRACTION99.89
2.01-2.070.28441360.20642594X-RAY DIFFRACTION99.93
2.07-2.140.25651370.20392598X-RAY DIFFRACTION100
2.14-2.210.2041380.17592627X-RAY DIFFRACTION100
2.21-2.30.24581360.18232572X-RAY DIFFRACTION100
2.3-2.410.23431370.17762618X-RAY DIFFRACTION100
2.41-2.530.21891370.17072602X-RAY DIFFRACTION100
2.53-2.690.21581380.17472625X-RAY DIFFRACTION100
2.69-2.90.19091380.17642624X-RAY DIFFRACTION100
2.9-3.190.20861390.16842632X-RAY DIFFRACTION99.96
3.19-3.650.19881400.15532658X-RAY DIFFRACTION99.57
3.65-4.60.14111410.13652690X-RAY DIFFRACTION100
4.6-46.590.15951490.1612810X-RAY DIFFRACTION99.9
Refinement TLS params.Method: refined / Origin x: -8.41075547974 Å / Origin y: -7.21932879309 Å / Origin z: -36.5094833432 Å
111213212223313233
T0.210536606332 Å2-0.0130366207973 Å20.00698922228808 Å2-0.179055431502 Å20.00312060239631 Å2--0.232567856046 Å2
L0.895726660098 °2-0.150713239043 °20.131755490185 °2-0.379190227515 °20.298015795566 °2--1.07230764625 °2
S-0.00901721743995 Å °0.00415206659973 Å °0.0430853289926 Å °0.0143575976578 Å °-0.0176506963217 Å °0.036328550634 Å °-0.0358737397998 Å °-0.0251892511807 Å °0.0221281890113 Å °
Refinement TLS groupSelection details: all

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