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- PDB-1h7z: Adenovirus Ad3 fibre head -

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Basic information

Entry
Database: PDB / ID: 1h7z
TitleAdenovirus Ad3 fibre head
ComponentsADENOVIRUS FIBRE PROTEIN
KeywordsCELL RECEPTOR RECOGNITION / ADENOVIRUS / AD3 / FIBRE / RECEPTOR
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, 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 / Sandwich / Mainly Beta
Similarity search - Domain/homology
Biological speciesHUMAN ADENOVIRUS TYPE 3
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsDurmort, C. / Stehlin, C. / Schoehn, G. / Mitraki, A. / Drouet, E. / Cusack, S. / Burmeister, W.P.
CitationJournal: Virology / Year: 2001
Title: Structure of the Fiber Head of Ad3, a Non-Car-Binding Serotype of Adenovirus
Authors: Durmort, C. / Stehlin, C. / Schoehn, G. / Mitraki, A. / Drouet, E. / Cusack, S. / Burmeister, W.P.
History
DepositionJan 21, 2001Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 19, 2001Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: ADENOVIRUS FIBRE PROTEIN
B: ADENOVIRUS FIBRE PROTEIN
C: ADENOVIRUS FIBRE PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,52511
Polymers64,7563
Non-polymers7698
Water16,051891
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)96.580, 96.580, 154.570
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(-0.1106, -0.2525, -0.9613), (-0.9196, 0.3929, 0.0026), (0.3771, 0.8842, -0.2756)13.6761, 20.0738, -22.2322
2given(-0.105, -0.9187, 0.3807), (-0.2613, 0.3949, 0.8808), (-0.9595, -0.007, -0.2815)28.5125, 15.0678, 7.633

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Components

#1: Protein ADENOVIRUS FIBRE PROTEIN


Mass: 21585.447 Da / Num. of mol.: 3 / Fragment: HEAD DOMAIN RESIDUES 126-319 / Mutation: YES
Source method: isolated from a genetically manipulated source
Details: ONLY THE HEAD DOMAIN, START CODON INTRODUCED AT POSITION 126
Source: (gene. exp.) HUMAN ADENOVIRUS TYPE 3 / Strain: AD3 / Plasmid: PACUW31 / Cellular location (production host): CYTOPLASM / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): JM109 (DE3) / References: UniProt: P04501
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 891 / Source method: isolated from a natural source / Formula: H2O
Compound detailsCHAIN A, B, C ENGINEERED MUTATION ILE126MET SERVES AS THE LIGAND BETWEEN THE ADENOVIRUS CAPSID AND ...CHAIN A, B, C ENGINEERED MUTATION ILE126MET SERVES AS THE LIGAND BETWEEN THE ADENOVIRUS CAPSID AND THE HOST CELL RECEPTOR.

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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: 3.51 Å3/Da / Density % sol: 64.7 %
Crystal growpH: 7
Details: RESERVOIR: 1.5 M LI2SO4, 0.1 M HEPES PH 7.0, 7.5 MG/ML PROTEIN IN 0.02 M TRIS-HCL PH 7.0 0.001 M EDTA, 0.02 M NACL
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
11.25 M1reservoiror 1.5MLi2SO4
20.1 MHEPES1reservoir
37.5 mg/mlprotein1drop

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.933
DetectorType: MARRESEARCH / Detector: CCD / Date: Aug 15, 2000 / Details: SAGITALLY FOCUSING 2ND CRYSTAL, MULTILAYER
RadiationMonochromator: DIAMOND(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.933 Å / Relative weight: 1
ReflectionResolution: 1.6→19.389 Å / Num. obs: 108500 / % possible obs: 98.6 % / Redundancy: 3.1 % / Biso Wilson estimate: 29.4 Å2 / Rmerge(I) obs: 0.045 / Rsym value: 0.045 / Net I/σ(I): 9
Reflection shellResolution: 1.6→1.69 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.331 / Mean I/σ(I) obs: 1.9 / Rsym value: 0.331 / % possible all: 97.9
Reflection shell
*PLUS
% possible obs: 97.9 %

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Processing

Software
NameClassification
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1KNB

1knb


Resolution: 1.6→19.96 Å / SU B: 1.56 / SU ML: 0.054 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.077 / ESU R Free: 0.084
Details: RESIDUES 219 - 224 ARE POORLY DEFINED. THE CONFORMATION OF RESIDUES 240 - 246 DIFFERS FOR THE THREE MONOMERS DUE TO A CRYSTAL CONTACT IN THIS REGION THE DENSITY MAPS ONLY SHOW RESIDUES STARTING FROM 129
RfactorNum. reflection% reflectionSelection details
Rfree0.216 5271 5 %RANDOM
Rwork0.176 ---
obs-105445 98.6 %-
Displacement parametersBiso mean: 36.9 Å2
Refinement stepCycle: LAST / Resolution: 1.6→19.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4497 0 40 891 5428
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0150.02
X-RAY DIFFRACTIONp_angle_d0.0350.04
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.0370.05
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it4.93
X-RAY DIFFRACTIONp_mcangle_it5.84
X-RAY DIFFRACTIONp_scbond_it6.54
X-RAY DIFFRACTIONp_scangle_it7.95
X-RAY DIFFRACTIONp_plane_restr
X-RAY DIFFRACTIONp_chiral_restr0.1750.15
X-RAY DIFFRACTIONp_singtor_nbd0.1820.3
X-RAY DIFFRACTIONp_multtor_nbd0.2630.3
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd0.120.3
X-RAY DIFFRACTIONp_planar_tor5.77
X-RAY DIFFRACTIONp_staggered_tor12.615
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor23.620
X-RAY DIFFRACTIONp_special_tor15
Software
*PLUS
Name: REFMAC / Classification: refinement
Refinement
*PLUS
Rfactor obs: 0.176
Solvent computation
*PLUS
Displacement parameters
*PLUS
LS refinement shell
*PLUS
Highest resolution: 1.6 Å / Lowest resolution: 1.69 Å / Rfactor Rfree: 0.284 / Rfactor obs: 0.256

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