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Yorodumi- PDB-2bse: Structure of Lactococcal Bacteriophage p2 Receptor Binding Protei... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2bse | ||||||
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Title | Structure of Lactococcal Bacteriophage p2 Receptor Binding Protein in complex with a llama VHH domain | ||||||
Components |
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Keywords | RECEPTOR / LACTOCOCCUS LACTIS / PHAGE / RECEPTOR BINDING PROTEIN / LLAMA ANTIBODY / VHH | ||||||
Function / homology | Function and homology information virus tail, baseplate / entry receptor-mediated virion attachment to host cell / cell adhesion / symbiont entry into host cell / virion attachment to host cell Similarity search - Function | ||||||
Biological species | LACTOCOCCUS VIRUS P2 LAMA GLAMA (llama) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å | ||||||
Authors | Spinelli, S. / Desmyter, A. / Verrips, C.T. / de Haard, H.J.W. / Moineau, S. / Cambillau, C. | ||||||
Citation | Journal: Nat.Struct.Mol.Biol. / Year: 2006 Title: Lactococcal Bacteriophage P2 Receptor Binding Protein Structure Suggests a Common Ancestor Gene with Bacterial and Mammalian Viruses. Authors: Spinelli, S. / Desmyter, A. / Verrips, C.T. / de Haard, H.J.W. / Moineau, S. / Cambillau, C. | ||||||
History |
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Remark 700 | SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2bse.cif.gz | 143.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2bse.ent.gz | 110.3 KB | Display | PDB format |
PDBx/mmJSON format | 2bse.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2bse_validation.pdf.gz | 463.1 KB | Display | wwPDB validaton report |
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Full document | 2bse_full_validation.pdf.gz | 479.5 KB | Display | |
Data in XML | 2bse_validation.xml.gz | 24.1 KB | Display | |
Data in CIF | 2bse_validation.cif.gz | 33.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bs/2bse ftp://data.pdbj.org/pub/pdb/validation_reports/bs/2bse | HTTPS FTP |
-Related structure data
Related structure data | 2bsdSC 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
#1: Protein | Mass: 28668.057 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) LACTOCOCCUS VIRUS P2 / Production host: ESCHERICHIA COLI K-12 (bacteria) / References: UniProt: Q71AW2 #2: Antibody | Mass: 13499.944 Da / Num. of mol.: 3 / Fragment: VHH RECOGNITION DOMAIN, RESIDUES 1-123 Source method: isolated from a genetically manipulated source Source: (gene. exp.) LAMA GLAMA (llama) / Cell: LYMPHOCYTE / Production host: SACCHAROMYCES CEREVISIAE (brewer's yeast) #3: 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: 2.95 Å3/Da |
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Crystal grow | pH: 6.5 / Details: pH 6.50 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.9794 |
Detector | Type: ADSC CCD / Detector: CCD |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9794 Å / Relative weight: 1 |
Reflection | Resolution: 2.7→15 Å / Num. obs: 23055 / % possible obs: 99 % / Observed criterion σ(I): 1 / Redundancy: 2.3 % / Rmerge(I) obs: 0.1 / Net I/σ(I): 5.6 |
Reflection shell | Resolution: 2.7→2.77 Å / Rmerge(I) obs: 0.3 / Mean I/σ(I) obs: 2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2BSD Resolution: 2.7→15 Å / Cor.coef. Fo:Fc: 0.907 / Cor.coef. Fo:Fc free: 0.884 / SU B: 16.719 / SU ML: 0.336 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 1.192 / ESU R Free: 0.388 / 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: 23.72 Å2
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Refinement step | Cycle: LAST / Resolution: 2.7→15 Å
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Refine LS restraints |
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