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Open data
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Basic information
Entry | Database: PDB / ID: 1h7z | ||||||
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Title | Adenovirus Ad3 fibre head | ||||||
![]() | ADENOVIRUS FIBRE PROTEIN | ||||||
![]() | CELL RECEPTOR RECOGNITION / ADENOVIRUS / AD3 / FIBRE / RECEPTOR | ||||||
Function / homology | ![]() 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 | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Durmort, C. / Stehlin, C. / Schoehn, G. / Mitraki, A. / Drouet, E. / Cusack, S. / Burmeister, W.P. | ||||||
![]() | ![]() 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 |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 144.8 KB | Display | ![]() |
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PDB format | ![]() | 114.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 459.3 KB | Display | ![]() |
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Full document | ![]() | 477.3 KB | Display | |
Data in XML | ![]() | 35.4 KB | Display | |
Data in CIF | ![]() | 53.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1knbS S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS oper:
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Components
#1: 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.) ![]() ![]() ![]() #2: Chemical | ChemComp-SO4 / #3: Water | ChemComp-HOH / | Compound details | CHAIN A, B, C ENGINEERED MUTATION ILE126MET SERVES AS THE LIGAND BETWEEN THE ADENOVIRUS CAPSID AND ...CHAIN A, B, C ENGINEERED | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.51 Å3/Da / Density % sol: 64.7 % | ||||||||||||||||||||||||||||
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Crystal grow | pH: 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
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Aug 15, 2000 / Details: SAGITALLY FOCUSING 2ND CRYSTAL, MULTILAYER |
Radiation | Monochromator: DIAMOND(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.933 Å / Relative weight: 1 |
Reflection | Resolution: 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 shell | Resolution: 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
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 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
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Displacement parameters | Biso mean: 36.9 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.6→19.96 Å
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Refine LS restraints |
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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 |