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- PDB-4liy: Structure of the adenovirus 3 knob domain K217E and F224S mutant -

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Basic information

Entry
Database: PDB / ID: 4liy
TitleStructure of the adenovirus 3 knob domain K217E and F224S mutant
ComponentsFiber protein
KeywordsVIRAL PROTEIN / adenovirus fibre protein knob domain / viral attachment to host cell / receptor interaction / desmoglein 2
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, 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 / Sandwich / Mainly Beta
Similarity search - Domain/homology
Biological speciesHuman adenovirus 3
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsZubieta, C. / Fender, P.
CitationJournal: J.Virol. / Year: 2013
Title: Structural and functional studies on the interaction of adenovirus fiber knobs and desmoglein 2
Authors: Wang, H. / Yumul, R. / Cao, H. / Ran, L. / Fan, X. / Richter, M. / Epstein, F. / Gralow, J. / Zubieta, C. / Fender, P. / Lieber, A.
History
DepositionJul 4, 2013Deposition site: RCSB / Processing site: PDBJ
Revision 1.0May 28, 2014Provider: repository / Type: Initial release
Revision 1.1Nov 8, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Fiber protein
B: Fiber protein
C: Fiber protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)83,5634
Polymers83,4673
Non-polymers961
Water4,900272
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5260 Å2
ΔGint-41 kcal/mol
Surface area22540 Å2
MethodPISA
Unit cell
Length a, b, c (Å)96.663, 96.663, 156.399
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein Fiber protein / SPIKE / Protein IV


Mass: 27822.396 Da / Num. of mol.: 3 / Fragment: knob domain, UNP residues 123-319 / Mutation: K217E, F224S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human adenovirus 3 / Gene: L5 / Plasmid: pQE30 / Production host: Escherichia coli (E. coli) / Strain (production host): XL1 Blue / References: UniProt: P04501
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 272 / 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: 2.53 Å3/Da / Density % sol: 51.33 %
Crystal growTemperature: 288 K / Method: vapor diffusion, hanging drop / pH: 9
Details: 1.65M MgSO4, 0.1M TAPS, pH 9, VAPOR DIFFUSION, HANGING DROP, temperature 288K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.97239 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: May 1, 2013
RadiationMonochromator: channel cut monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97239 Å / Relative weight: 1
ReflectionResolution: 2.1→48.332 Å / Num. all: 49985 / Num. obs: 49786 / % possible obs: 99.6 % / Observed criterion σ(F): 1.5 / Observed criterion σ(I): 1.5 / Redundancy: 4.4 % / Biso Wilson estimate: 46 Å2 / Rmerge(I) obs: 0.081 / Rsym value: 0.072 / Net I/σ(I): 11.46
Reflection shellResolution: 2.1→2.15 Å / Redundancy: 4.3 % / Rmerge(I) obs: 0.632 / Mean I/σ(I) obs: 1.79 / Num. unique all: 3607 / Rsym value: 0.719 / % possible all: 98.6

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Processing

Software
NameVersionClassification
DNAdata collection
PHASERphasing
PHENIX(phenix.refine: dev_1391)refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1H7Z

1h7z


Resolution: 2.1→48.332 Å / Occupancy max: 1 / Occupancy min: 0.48 / SU ML: 0.22 / Cross valid method: throughput / σ(F): 1.34 / Phase error: 20.22 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2012 2528 5.08 %random
Rwork0.1759 ---
all0.2012 49756 --
obs0.1772 49756 99.55 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 133.53 Å2 / Biso mean: 49.9725 Å2 / Biso min: 20 Å2
Refinement stepCycle: LAST / Resolution: 2.1→48.332 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4304 0 5 272 4581
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0124453
X-RAY DIFFRACTIONf_angle_d1.3066075
X-RAY DIFFRACTIONf_chiral_restr0.073695
X-RAY DIFFRACTIONf_plane_restr0.005780
X-RAY DIFFRACTIONf_dihedral_angle_d12.5981593
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 18

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.1-2.14040.30791460.26322525267198
2.1404-2.18410.29741540.259225722726100
2.1841-2.23160.26391420.24052552269499
2.2316-2.28350.24391320.217526002732100
2.2835-2.34060.251360.206926242760100
2.3406-2.40390.25191350.206625952730100
2.4039-2.47460.24431230.19822588271199
2.4746-2.55450.23761620.195526092771100
2.5545-2.64580.22031260.192326162742100
2.6458-2.75170.22071420.182426292771100
2.7517-2.87690.21491400.18725922732100
2.8769-3.02860.20231420.18432635277799
3.0286-3.21830.19181300.18726342764100
3.2183-3.46670.20331610.173126112772100
3.4667-3.81550.19951390.164226692808100
3.8155-4.36730.15671310.143426572788100
4.3673-5.50110.14681330.134526982831100
5.5011-48.34440.21071540.18942822297699
Refinement TLS params.Method: refined / Origin x: 38.7172 Å / Origin y: -36.5109 Å / Origin z: 12.9515 Å
111213212223313233
T0.2356 Å20.0478 Å20.0112 Å2-0.3233 Å20.0012 Å2--0.2913 Å2
L1.0865 °20.3091 °2-0.1994 °2-0.8699 °2-0.3501 °2--1.0489 °2
S0.0046 Å °0.0586 Å °-0.0546 Å °-0.0198 Å °0.0146 Å °0.0043 Å °-0.0486 Å °-0.1334 Å °-0.0008 Å °
Refinement TLS groupSelection details: ALL

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