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Yorodumi- PDB-1n7u: THE RECEPTOR-BINDING PROTEIN P2 OF BACTERIOPHAGE PRD1: CRYSTAL FORM I -
+Open data
-Basic information
Entry | Database: PDB / ID: 1n7u | ||||||
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Title | THE RECEPTOR-BINDING PROTEIN P2 OF BACTERIOPHAGE PRD1: CRYSTAL FORM I | ||||||
Components | Adsorption protein P2 | ||||||
Keywords | VIRAL PROTEIN / bacteriophage PRD1 / viral receptor-binding / beta-propeller / proline-rich / antibiotic-resistance | ||||||
Function / homology | Function and homology information virion component / symbiont entry into host cell / virion attachment to host cell Similarity search - Function | ||||||
Biological species | Enterobacteria phage PRD1 (virus) | ||||||
Method | X-RAY DIFFRACTION / MAD / Resolution: 2.4 Å | ||||||
Authors | Xu, L. / Benson, S.D. / Butcher, S.J. / Bamford, D.H. / Burnett, R.M. | ||||||
Citation | Journal: Structure / Year: 2003 Title: The Receptor Binding Protein P2 of PRD1, a Virus Targeting Antibiotic-Resistant Bacteria, Has a Novel Fold Suggesting Multiple Functions. Authors: Xu, L. / Benson, S.D. / Butcher, S.J. / Bamford, D.H. / Burnett, R.M. #1: Journal: J.STRUCT.BIOL. / Year: 2000 Title: Crystallization and preliminary X-ray analysis of receptor-binding protein P2 of bacteriopahge PRD1 Authors: Xu, L. / Butcher, S.J. / Benson, S.D. / Bamford, D.H. / Burnett, R.M. #2: Journal: J.BACTERIOL. / Year: 1999 Title: Stable packing of phage PRD1 DNA requires adsorption protein P2, which binds to the IncP plasmid-encoded conjugative transfer complex Authors: Grahn, A.M. / Caldentey, J. / Bamford, J.K.H. / Bamford, D.H. #3: Journal: Adv.Virus Res. / Year: 1995 Title: Bacteriophage PRD1: a broad host range dsDNA tectivirus with an internal membrane Authors: Bamford, D.H. / Caldentey, J. / Bamford, J.K.H. #4: Journal: Cell(Cambridge,Mass.) / Year: 1999 Title: Viral evolution revealed by bacteriophage PRD1 and human adenovirus coat protein structures Authors: Benson, S.D. / Bamford, J.K.H. / Bamford, D.H. / Burnett, R.M. #5: Journal: J.Mol.Biol. / Year: 1999 Title: Bacteriophage PRD1 contains a labile receptor-binding structure at each vertex Authors: Rydman, P.S. / Caldentey, J. / Butcher, S.J. / Fuller, S.D. / Rutten, T. / Bamford, D.H. #6: Journal: Thesis / Year: 2002 Title: A tale of two viruses with therapeutic potential: Structural studies on CELO, an avian adenovirus and the bacteriophage PRD1 Authors: Xu, L. | ||||||
History |
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Remark 351 | The biomolecule is most probably a monomer. Nevertheless, it is notable that the same dimer ... The biomolecule is most probably a monomer. Nevertheless, it is notable that the same dimer appears in the two crystal forms (1N7U and 1N7V). Although the buried surface per subunit in the dimer is ~1,206 A**2, which is relatively substantial, it only represents ~5.5% of the surface area of the P2 monomer. Rate zonal centrifugation, gel filtration, cross-linking, sedimentation equilibrium and low angle X-ray scattering strongly suggest that P2 is a monomer in solution. Furthermore, dynamic light scattering measurements indicated a monodisperse solution with an apparent molecular weight of 79 kDa, which is in reasonable agreement with that for the monomer (63.9 kDa). Nevertheless, P2 may form a loosely associated dimer when bound to the virion. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1n7u.cif.gz | 124.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1n7u.ent.gz | 94.1 KB | Display | PDB format |
PDBx/mmJSON format | 1n7u.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/n7/1n7u ftp://data.pdbj.org/pub/pdb/validation_reports/n7/1n7u | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Details | Biochemical evidence (gel filtration, low angle X-ray scattering, rate-zonal ultracentrifugation, and dynamic light scattering) indicate that P2 is monomeric, but a potential dimer appears in 3 crystal with different space groups and is obtained for this crystal form by the following symmetry operation: x, -y, -z |
-Components
#1: Protein | Mass: 59828.297 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Enterobacteria phage PRD1 (virus) / Genus: Tectivirus / Gene: II / Plasmid: pMG59 / Production host: Escherichia coli (E. coli) / Strain (production host): HMS174 / References: UniProt: P27378 | ||||
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#2: Chemical | #3: Chemical | ChemComp-CA / | #4: 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: 3.57 Å3/Da / Density % sol: 65.3 % | ||||||||||||||||||||||||||||
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop, macroseeding / pH: 4.6 Details: 30% MPD, 0.1 M sodium acetate, 20 mM CaCl2, pH 4.6, VAPOR DIFFUSION, HANGING DROP, MACROSEEDING, temperature 277K | ||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 4 ℃ / Method: vapor diffusion, hanging drop / Details: used macroseeding | ||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å |
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Dec 13, 2001 / Details: mirrors |
Radiation | Monochromator: Yale mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.4→43 Å / Num. all: 35306 / Num. obs: 32726 / % possible obs: 92.7 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 9 % / Biso Wilson estimate: 26.2 Å2 / Rsym value: 0.071 / Net I/σ(I): 12 |
Reflection shell | Resolution: 2.4→2.55 Å / Num. unique all: 3550 / Rsym value: 0.477 / % possible all: 61.5 |
Reflection | *PLUS Rmerge(I) obs: 0.071 |
Reflection shell | *PLUS % possible obs: 78.7 % / Rmerge(I) obs: 0.477 / Mean I/σ(I) obs: 2.1 |
-Processing
Software |
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Refinement | Method to determine structure: MAD Starting model: Se-Met P2 Resolution: 2.4→43.22 Å / Rfactor Rfree error: 0.007 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 32.4238 Å2 / ksol: 0.294665 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 46 Å2
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Refine analyze | Luzzati coordinate error free: 0.39 Å / Luzzati sigma a free: 0.44 Å | ||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.4→43.22 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.4→2.55 Å / Rfactor Rfree error: 0.057 / Total num. of bins used: 6
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Xplor file |
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Refinement | *PLUS Highest resolution: 2.4 Å | ||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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