+Open data
-Basic information
Entry | Database: PDB / ID: 1yu0 | ||||||
---|---|---|---|---|---|---|---|
Title | Major Tropism Determinant P1 Variant | ||||||
Components | Major Tropism Determinant (Mtd-P1) | ||||||
Keywords | VIRAL PROTEIN / C-type Lectin / Beta Sandwich / Beta Prism / variability / diversity-generating retroelement | ||||||
Function / homology | Function and homology information viral tropism switching / virus tail, fiber / adhesion receptor-mediated virion attachment to host cell / symbiont entry into host cell Similarity search - Function | ||||||
Biological species | Bordetella phage BPP-1 (virus) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.56 Å | ||||||
Authors | McMahon, S.A. / Miller, J.L. / Lawton, J.A. / Ghosh, P. | ||||||
Citation | Journal: Nat.Struct.Mol.Biol. / Year: 2005 Title: The C-type lectin fold as an evolutionary solution for massive sequence variation Authors: McMahon, S.A. / Miller, J.L. / Lawton, J.A. / Kerkow, D.E. / Hodes, A. / Marti-Renom, M.A. / Doulatov, S. / Narayanan, E. / Sali, A. / Miller, J.F. / Ghosh, P. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 1yu0.cif.gz | 93.5 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb1yu0.ent.gz | 69.7 KB | Display | PDB format |
PDBx/mmJSON format | 1yu0.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1yu0_validation.pdf.gz | 417.3 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 1yu0_full_validation.pdf.gz | 417.8 KB | Display | |
Data in XML | 1yu0_validation.xml.gz | 19 KB | Display | |
Data in CIF | 1yu0_validation.cif.gz | 30.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yu/1yu0 ftp://data.pdbj.org/pub/pdb/validation_reports/yu/1yu0 | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
| ||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||||||||||||
Unit cell |
| ||||||||||||||||||
Components on special symmetry positions |
| ||||||||||||||||||
Details | The biological assembly is a trimer generated from: -y, x-y, z and -x+y, -x, z |
-Components
#1: Protein | Mass: 39557.484 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bordetella phage BPP-1 (virus) / Plasmid: pGEX / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / References: UniProt: Q775D6 | ||
---|---|---|---|
#2: Chemical | #3: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 3.1 Å3/Da / Density % sol: 60.8 % |
---|---|
Crystal grow | Temperature: 298 K / Method: vapor diffusion / pH: 7.5 Details: PEG 550 MME, HEPES, calcium chloride, pH 7.5, VAPOR DIFFUSION, temperature 298K |
-Data collection
Diffraction |
| |||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Diffraction source |
| |||||||||||||||
Radiation |
| |||||||||||||||
Radiation wavelength |
| |||||||||||||||
Reflection | Resolution: 1.56→50 Å / Num. all: 69212 / Num. obs: 69212 / % possible obs: 98.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 | |||||||||||||||
Reflection shell | Resolution: 1.56→1.62 Å / % possible all: 100 |
-Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MAD / Resolution: 1.56→20.33 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.961 / SU B: 0.693 / SU ML: 0.026 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.05 / ESU R Free: 0.051 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 8.629 Å2
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.56→20.33 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 1.56→1.599 Å / Total num. of bins used: 20
|