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Yorodumi- PDB-2fsd: A Common Fold for the Receptor Binding Domains of Lactococcal Pha... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2fsd | ||||||
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Title | A Common Fold for the Receptor Binding Domains of Lactococcal Phages? The Crystal Structure of the Head Domain of Phage bIL170 | ||||||
Components | putative baseplate protein | ||||||
Keywords | VIRAL PROTEIN / Phage / Lactococcus lactis / receptor binding protein / head domain | ||||||
Function / homology | Phage bIL170 RBP, head domain / Phage bIL170 RBP, head domain / Receptor-binding protein of phage tail base-plate Siphoviridae, head / Lactophage receptor-binding protein C-terminal head domain / Immunoglobulin-like / Sandwich / Mainly Beta / Putative baseplate protein Function and homology information | ||||||
Biological species | unidentified phage (virus) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.3 Å | ||||||
Authors | Ricagno, S. / Cambillau, C. | ||||||
Citation | Journal: J.Virol. / Year: 2006 Title: Crystal Structure of the Receptor-Binding Protein Head Domain from Lactococcus lactis Phage bIL170 Authors: Ricagno, S. / Campanacci, V. / Blangy, S. / Spinelli, S. / Tremblay, D. / Moineau, S. / Tegoni, M. / Cambillau, C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2fsd.cif.gz | 54.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2fsd.ent.gz | 38.9 KB | Display | PDB format |
PDBx/mmJSON format | 2fsd.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2fsd_validation.pdf.gz | 437.3 KB | Display | wwPDB validaton report |
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Full document | 2fsd_full_validation.pdf.gz | 438.4 KB | Display | |
Data in XML | 2fsd_validation.xml.gz | 10.7 KB | Display | |
Data in CIF | 2fsd_validation.cif.gz | 14.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fs/2fsd ftp://data.pdbj.org/pub/pdb/validation_reports/fs/2fsd | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Details | The biological assembly is a trimer. The crystal assymmetric unit contains a dimer |
-Components
#1: Protein | Mass: 15284.188 Da / Num. of mol.: 2 / Fragment: RBP head domain, Residues 1-113 Source method: isolated from a genetically manipulated source Source: (gene. exp.) unidentified phage (virus) / Strain: bIL170 / Production host: Escherichia coli (E. coli) / References: UniProt: O80120 #2: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.18 Å3/Da / Density % sol: 43.65 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 5.5 Details: nanodrop setting (300 nL), pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 291K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-3 / Wavelength: 0.931 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Sep 20, 2005 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.931 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→32.7 Å / Num. all: 12327 / Num. obs: 12327 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 |
Reflection shell | Resolution: 2.3→2.42 Å / % possible all: 99.7 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 2.3→23.8 Å / Cor.coef. Fo:Fc: 0.873 / Cor.coef. Fo:Fc free: 0.86 / SU B: 7.333 / SU ML: 0.185 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.335 / ESU R Free: 0.24 / 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: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 20.229 Å2
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Refine analyze | Luzzati coordinate error free: 0.24 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.3→23.8 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.3→2.359 Å / Total num. of bins used: 20
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