+Open data
-Basic information
Entry | Database: PDB / ID: 1yu2 | ||||||
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Title | Major Tropism Determinant M1 Variant | ||||||
Components | Major Tropism Determinant (Mtd-M1) | ||||||
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 BMP-1 (virus) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.86 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 |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1yu2.cif.gz | 89.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1yu2.ent.gz | 66.3 KB | Display | PDB format |
PDBx/mmJSON format | 1yu2.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1yu2_validation.pdf.gz | 420.3 KB | Display | wwPDB validaton report |
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Full document | 1yu2_full_validation.pdf.gz | 421.5 KB | Display | |
Data in XML | 1yu2_validation.xml.gz | 18 KB | Display | |
Data in CIF | 1yu2_validation.cif.gz | 27.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yu/1yu2 ftp://data.pdbj.org/pub/pdb/validation_reports/yu/1yu2 | HTTPS FTP |
-Related structure data
Related structure data | 1yu0SC 1yu1C 1yu3C 1yu4C S: Starting model for refinement C: citing same article (ref.) |
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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 biological assembly is a trimer generated from: -y, x-y, z and -x+y, -x, z |
-Components
#1: Protein | Mass: 39604.395 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bordetella phage BMP-1 (virus) / Plasmid: pET / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / References: UniProt: Q775D6 |
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#2: Chemical | ChemComp-MG / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.1 Å3/Da / Density % sol: 60.8 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion / pH: 7.5 Details: Isopropanol, Sodium Citrate, HEPES, pH 7.5, VAPOR DIFFUSION, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5479 Å |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5479 Å / Relative weight: 1 |
Reflection | Resolution: 1.86→50 Å / Num. all: 42618 / Num. obs: 42618 / % possible obs: 98.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 |
Reflection shell | Resolution: 1.86→1.92 Å / % possible all: 85.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 1YU0 Resolution: 1.86→42.64 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.958 / SU B: 1.963 / SU ML: 0.059 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.103 / ESU R Free: 0.094 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 19.552 Å2
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Refinement step | Cycle: LAST / Resolution: 1.86→42.64 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.857→1.905 Å / Total num. of bins used: 20 /
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