+Open data
-Basic information
Entry | Database: PDB / ID: 1qhv | ||||||
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Title | HUMAN ADENOVIRUS SEROTYPE 2 FIBRE HEAD | ||||||
Components | PROTEIN (ADENOVIRUS FIBRE) | ||||||
Keywords | VIRAL PROTEIN / RECEPTOR BINDING / EXTRA-ORDINARY STABILITY | ||||||
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 | ||||||
Biological species | Human adenovirus 2 | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.51 Å | ||||||
Authors | Van Raaij, M.J. / Louis, N. / Chroboczek, J. / Cusack, S. | ||||||
Citation | Journal: Virology / Year: 1999 Title: Structure of the human adenovirus serotype 2 fiber head domain at 1.5 A resolution. Authors: van Raaij, M.J. / Louis, N. / Chroboczek, J. / Cusack, S. #1: Journal: J.Virol. / Year: 1994 Title: Cell-Binding Domain of Adenovirus Serotype 2 Fiber Authors: Louis, N. / Fender, P. / Barge, A. / Kitts, P. / Chroboczek, J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1qhv.cif.gz | 102.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1qhv.ent.gz | 78.3 KB | Display | PDB format |
PDBx/mmJSON format | 1qhv.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1qhv_validation.pdf.gz | 430.4 KB | Display | wwPDB validaton report |
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Full document | 1qhv_full_validation.pdf.gz | 430.4 KB | Display | |
Data in XML | 1qhv_validation.xml.gz | 12.4 KB | Display | |
Data in CIF | 1qhv_validation.cif.gz | 19 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qh/1qhv ftp://data.pdbj.org/pub/pdb/validation_reports/qh/1qhv | HTTPS FTP |
-Related structure data
Related structure data | 1knbS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Components on special symmetry positions |
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Details | THE FUNCTIONAL MOLECULE IS A TRIMER. THIS TRIMER IS GENERATED USING THE THREE-FOLD AXIS SYMMETRY. |
-Components
#1: Protein | Mass: 21478.893 Da / Num. of mol.: 1 / Fragment: HEAD DOMAIN Source method: isolated from a genetically manipulated source Source: (gene. exp.) Human adenovirus 2 / Genus: Mastadenovirus / Species: Human adenovirus C / Strain: SEROTYPE 2 / Gene: LOCUS AD2H2 / Plasmid: PACCL29 / Production host: Spodoptera frugiperda (fall armyworm) / Strain (production host): SF9 / References: UniProt: Q96590, UniProt: P03275*PLUS | ||
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#2: Chemical | #3: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 3 |
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-Sample preparation
Crystal | Density Matthews: 2.96 Å3/Da / Density % sol: 58 % | |||||||||||||||||||||||||||||||||||
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Crystal grow | pH: 4 Details: 100 MM SODIUM ACETATE 25 % (V/V) GLYCEROL 1-1.5 M AMMONIUM SULPHATE PH 4.0 WITH ACETIC ACID | |||||||||||||||||||||||||||||||||||
Crystal | *PLUS | |||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 20 ℃ / Method: vapor diffusion, sitting drop / PH range low: 5.2 / PH range high: 4 | |||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID2 / Wavelength: 0.993 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Apr 1, 1997 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.993 Å / Relative weight: 1 |
Reflection | Resolution: 1.51→10.97 Å / Num. obs: 36820 / % possible obs: 91.8 % / Redundancy: 4.7 % / Biso Wilson estimate: 13.2 Å2 / Rsym value: 0.073 / Net I/σ(I): 7.3 |
Reflection shell | Resolution: 1.51→1.59 Å / Redundancy: 1.4 % / Mean I/σ(I) obs: 3.6 / Rsym value: 0.172 / % possible all: 55.3 |
Reflection | *PLUS Num. measured all: 386827 / Rmerge(I) obs: 0.073 |
Reflection shell | *PLUS % possible obs: 55.3 % / Num. unique obs: 3170 / Rmerge(I) obs: 0.172 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1KNB Resolution: 1.51→10.97 Å / SU B: 0.80142 / SU ML: 0.02897 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.05292 / ESU R Free: 0.05087
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Displacement parameters | Biso mean: 23.07 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.51→10.97 Å
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Refine LS restraints |
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Software | *PLUS Name: REFMAC / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS % reflection Rfree: 3 % / Rfactor obs: 0.109 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor Rfree: 0.18 / Rfactor obs: 0.136 |