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Yorodumi- PDB-1ifp: INOVIRUS (FILAMENTOUS BACTERIOPHAGE) STRAIN PF3 MAJOR COAT PROTEI... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1ifp | ||||||
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Title | INOVIRUS (FILAMENTOUS BACTERIOPHAGE) STRAIN PF3 MAJOR COAT PROTEIN ASSEMBLY | ||||||
Components | MAJOR COAT PROTEIN ASSEMBLY | ||||||
Keywords | VIRUS / VIRUS COAT PROTEIN / Helical virus | ||||||
Function / homology | Function and homology information helical viral capsid / membrane => GO:0016020 / host cell plasma membrane Similarity search - Function | ||||||
Biological species | Pseudomonas phage Pf3 (virus) | ||||||
Method | FIBER DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.1 Å | ||||||
Authors | Welsh, L.C. / Symmons, M.F. / Perham, R.N. / Marvin, D.A. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 1998 Title: Structure of the capsid of Pf3 filamentous phage determined from X-ray fibre diffraction data at 3.1 A resolution. Authors: Welsh, L.C. / Symmons, M.F. / Sturtevant, J.M. / Marvin, D.A. / Perham, R.N. #1: Journal: Acta Crystallogr.,Sect.D / Year: 1995 Title: Pf1 Filamentous Bacteriophage: Refinement of a Molecular Model by Simulated Annealing Using 3.3 A Resolution X-Ray Fibre Diffraction Data Authors: Gonzalez, A. / Nave, C. / Marvin, D.A. #2: Journal: Phase Transitions / Year: 1992 Title: Two Forms of Pf1 Inovirus: X-Ray Diffraction Studies on a Structural Phase Transition and a Calculated Libration Normal Mode of the Asymmetric Unit Authors: Marvin, D.A. / Nave, C. / Bansal, M. / Hale, R.D. / Salje, E.K.H. #3: Journal: Int.J.Biol.Macromol. / Year: 1990 Title: Model-Building Studies of Inovirus: Genetic Variations on a Geometric Theme Authors: Marvin, D.A. #4: Journal: Int.J.Biol.Macromol. / Year: 1990 Title: Erratum. Model-Building Studies of Inovirus: Genetic Variations on a Geometric Theme Authors: Marvin, D.A. #5: Journal: Int.J.Biol.Macromol. / Year: 1989 Title: Dynamics of Telescoping Inovirus: A Mechanism for Assembly at Membrane Adhesions Authors: Marvin, D.A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1ifp.cif.gz | 17.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1ifp.ent.gz | 10.4 KB | Display | PDB format |
PDBx/mmJSON format | 1ifp.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1ifp_validation.pdf.gz | 322.2 KB | Display | wwPDB validaton report |
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Full document | 1ifp_full_validation.pdf.gz | 322.2 KB | Display | |
Data in XML | 1ifp_validation.xml.gz | 2.1 KB | Display | |
Data in CIF | 1ifp_validation.cif.gz | 2.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/if/1ifp ftp://data.pdbj.org/pub/pdb/validation_reports/if/1ifp | HTTPS FTP |
-Related structure data
Related structure data | 1ifnS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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3 |
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Unit cell |
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Symmetry | Helical symmetry: (Circular symmetry: 1 / Dyad axis: no / N subunits divisor: 1 / Num. of operations: 35 / Rise per n subunits: 2.9 Å / Rotation per n subunits: 65.667 °) |
-Components
#1: Protein/peptide | Mass: 4632.466 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas phage Pf3 (virus) / Genus: Inovirus / Strain: NEW YORK / Description: FILAMENTOUS BACTERIOPHAGE / Production host: Pseudomonas aeruginosa (bacteria) / References: UniProt: P03623 |
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-Experimental details
-Experiment
Experiment | Method: FIBER DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal grow | pH: 7 / Details: pH 7.0 |
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Crystal grow | *PLUS Method: vapor diffusion |
Components of the solutions | *PLUS Conc.: 30 mg/ml / Common name: protein |
-Data collection
Diffraction | Mean temperature: 298 K |
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Diffraction source | Source: SYNCHROTRON / Site: SRS / Beamline: PX7.2 / Wavelength: 1.488 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Dec 1, 1995 / Details: MIRRORS |
Radiation | Monochromator: GE(111) / Monochromatic (M) / Laue (L): M |
Radiation wavelength | Wavelength: 1.488 Å / Relative weight: 1 |
Reflection | Resolution: 3.1→60 Å |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1IFN Resolution: 3.1→12 Å / Rfactor Rfree error: 0.01 / Cross valid method: A POSTERIORI Details: MODEL REFINED WITH A VERSION OF X-PLOR 3.1 MODIFIED FOR USE WITH FIBRE DIFFRACTION DATA BY WANG & STUBBS (1993) ACTA CRYST. A49, 504-513.
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Displacement parameters | Biso mean: 19 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.1→12 Å
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Refine LS restraints |
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Refine LS restraints NCS | NCS model details: STRICT NCS WAS IMPOSED ON THE MODEL THROUGHOUT THE REFINEMENT. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 3.1→3.43 Å / Total num. of bins used: 4 /
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Xplor file |
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Software | *PLUS Name: X-PLOR / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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