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- PDB-2qlk: Adenovirus AD35 fibre head -

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ID or keywords:

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Basic information

Entry
Database: PDB / ID: 2qlk
TitleAdenovirus AD35 fibre head
ComponentsFiber
KeywordsVIRAL PROTEIN / adenovirus / AD35 / Fibre / CD46-bindning
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 / 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 35
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.02 Å
AuthorsLiaw, Y.-C. / Amiraslanov, I. / Wang, H. / Lieber, A.
CitationJournal: J.Virol. / Year: 2007
Title: Identification of CD46 binding sites within the adenovirus serotype 35 fiber knob
Authors: Wang, H. / Liaw, Y.C. / Stone, D. / Kalyuzhniy, O. / Amiraslanov, I. / Tuve, S. / Verlinde, C.L. / Shayakhmetov, D. / Stehle, T. / Roffler, S. / Lieber, A.
History
DepositionJul 13, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 19, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.2Oct 18, 2017Group: Refinement description / Category: software
Revision 1.3Aug 30, 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,7502
Polymers23,6581
Non-polymers921
Water1,13563
1
A: Fiber
hetero molecules

A: Fiber
hetero molecules

A: Fiber
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,2516
Polymers70,9753
Non-polymers2763
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_555-x+y,-x,z1
crystal symmetry operation2_555-y,x-y,z1
Buried area6680 Å2
MethodPISA
Unit cell
Length a, b, c (Å)87.831, 87.831, 53.897
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number146
Space group name H-MH3

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Components

#1: Protein Fiber / PIV


Mass: 23658.299 Da / Num. of mol.: 1 / Fragment: head domain residues 123-323
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human adenovirus 35 / Genus: Mastadenovirus / Species: Human adenovirus B / Strain: AD35 / Plasmid: pQE30 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q67733, UniProt: Q7T925*PLUS
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 63 / 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

Crystal
IDDensity Matthews (Å3/Da)Density % sol (%)
11.6927.3
25.175.6
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 8
Details: Protein in 20mM Tris-HCl, 200mM NaCl, 5mM DTT, reservoir: 30% PEG1000, 0.2M MgBr2, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 294K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONNSRRC BL13B111
SYNCHROTRONNSRRC BL13C121
Detector
TypeIDDetectorDate
ADSC QUANTUM 3151CCDJan 1, 2007
ADSC QUANTUM 2102CCDJan 1, 2007
RadiationMonochromator: Si (1,1,1) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.02→30 Å / Num. all: 9568 / Num. obs: 9568 / % possible obs: 92.8 % / Redundancy: 4.7 % / Biso Wilson estimate: 10.1 Å2 / Rmerge(I) obs: 0.082 / Χ2: 1.067 / Net I/σ(I): 9.4
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.02-2.092.30.5016001.089158
2.09-2.182.90.4068401.078182.1
2.18-2.273.60.3739291.098190
2.27-2.394.20.33910191.084198.2
2.39-2.5450.28410181.0911100
2.54-2.745.40.20510341.0741100
2.74-3.025.60.12310271.0911100
3.02-3.455.60.08410361.0331100
3.45-4.355.50.05410311.0211100
4.35-305.40.04310341.0571100

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Phasing

PhasingMethod: molecular replacement
Phasing MRRfactor: 0.344 / Cor.coef. Fo:Fc: 0.665
Highest resolutionLowest resolution
Translation4 Å15 Å

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
EPMR2.5phasing
CNSrefinement
PDB_EXTRACT2data extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1H7Z

1h7z


Resolution: 2.02→25.4 Å / FOM work R set: 0.815 / Isotropic thermal model: restrained / Cross valid method: throughtout / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.257 946 9.3 %random
Rwork0.2 ---
all0.216 9049 --
obs0.216 9049 89.2 %-
Solvent computationBsol: 73.282 Å2
Displacement parametersBiso mean: 44.853 Å2
Baniso -1Baniso -2Baniso -3
1--7.54 Å20 Å20 Å2
2---7.54 Å20 Å2
3---15.079 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.31 Å0.24 Å
Luzzati d res low-5 Å
Luzzati sigma a0.3 Å0.28 Å
Refinement stepCycle: LAST / Resolution: 2.02→25.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1435 0 6 63 1504
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.01
X-RAY DIFFRACTIONc_angle_deg1.55
X-RAY DIFFRACTIONc_dihedral_angle_d26.6
X-RAY DIFFRACTIONc_improper_angle_d0.92
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection obs
2.02-2.060.397240.297249273
2.06-2.10.289430.284324367
2.1-2.150.273370.256395432
2.15-2.20.318430.235380423
2.2-2.250.306480.261413461
2.25-2.310.28440.231459503
2.31-2.380.275470.247463510
2.38-2.460.368450.257489534
2.46-2.550.29600.249451511
2.55-2.650.322660.222488554
2.65-2.770.265530.208499552
2.77-2.910.281620.203482544
2.91-3.10.276670.203500567
3.1-3.330.24610.185499560
3.33-3.670.234810.166487568
3.67-4.20.213610.161493554
4.2-5.290.213430.17531574
5.29-500.010.251610.206501562
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1protein_rep.param
X-RAY DIFFRACTION2gol.par
X-RAY DIFFRACTION3water_rep.param
X-RAY DIFFRACTION4ion.param

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