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Yorodumi- PDB-1ql2: Inovirus (Filamentous Bacteriophage) Strain PF1 Major Coat Protei... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1ql2 | ||||||
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Title | Inovirus (Filamentous Bacteriophage) Strain PF1 Major Coat Protein Assembly | ||||||
Components | PF1 BACTERIOPHAGE COAT PROTEIN B | ||||||
Keywords | VIRUS / VIRUS COAT PROTEIN / HELICAL VIRUS COAT PROTEIN / SSDNA VIRUSES / INOVIRUS / HELICAL VIRUS | ||||||
Function / homology | Function and homology information | ||||||
Biological species | PSEUDOMONAS PHAGE PF1 (virus) | ||||||
Method | FIBER DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.1 Å | ||||||
Authors | Welsh, L.C. / Symmons, M.F. / Marvin, D.A. | ||||||
Citation | Journal: Acta Crystallogr.,Sect.D / Year: 2000 Title: The Molecular Structure and Structural Transition of the Alpha-Helical Capsid in Filamentous Bacteriophage Pf1 Authors: Welsh, L.C. / Symmons, M.F. / Marvin, D.A. #1: Journal: Acta Crystallogr.,Sect.D / Year: 1995 Title: Pf1 Filamentous Bacteriophage: Refinement of a Molecular Model by Simulated Annealing Using 3.3 Angstroms 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: 1989 Title: Dynamics of Telescoping Inovirus: A Mechanism for Assembly at Membrane Adhesions Authors: Marvin, D.A. | ||||||
History |
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Remark 285 | THE ANALOGUE OF THE CRYSTALLOGRAPHIC SPACE GROUP FOR HELICAL STRUCTURES IS THE LINE GROUP (A.KLUG, ... THE ANALOGUE OF THE CRYSTALLOGRAPHIC SPACE GROUP FOR HELICAL STRUCTURES IS THE LINE GROUP (A.KLUG, F.H.C.CRICK, H.W.WYCKOFF, ACTA CRYSTALLOG. V.11, 199, 1958). THE LINE GROUP OF PF1 IS S. THE UNIT CELL DIMENSIONS ARE THE HELIX PARAMETERS (UNIT TWIST TAU, UNIT HEIGHT P). FOR THE PERTURBED MODEL OF PF1, TAU = 200. DEGREES, P = 8.70 ANGSTROMS. THE INDEXING OF UNITS ALONG THE BASIC HELIX IS ILLUSTRATED IN REFERENCE 4. TO GENERATE COORDINATES X(K), Y(K), Z(K) OF UNIT K FROM THE GIVEN COORDINATES X(0), Y(0), Z(0) OF UNIT 0 IN A UNIT CELL WITH HELIX PARAMETERS (TAU, P) = (66.667, 2.90), APPLY THE MATRIX AND VECTOR: | COS(TAU*K) -SIN(TAU*K) 0 | | 0 | | SIN(TAU*K) COS(TAU*K) 0 | + | 0 | | 0 0 1 | | P*K | THE NEIGHBORS IN CONTACT WITH UNIT 0 ARE UNITS K = +/-1, +/-5, +/-6, +/-11 AND +/-17. THESE SYMMETRY-RELATED COPIES ARE USED TO DETERMINE INTERCHAIN NON-BONDED CONTACTS DURING THE REFINEMENT. [ THE LOWER-TEMPERATURE FORM OF PF1 HAS HELIX PARAMETERS, TAU = 65.915 DEGREES, P = 3.05 ANGSTROMS. ] |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1ql2.cif.gz | 30.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1ql2.ent.gz | 22.4 KB | Display | PDB format |
PDBx/mmJSON format | 1ql2.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1ql2_validation.pdf.gz | 339.9 KB | Display | wwPDB validaton report |
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Full document | 1ql2_full_validation.pdf.gz | 341.6 KB | Display | |
Data in XML | 1ql2_validation.xml.gz | 3.9 KB | Display | |
Data in CIF | 1ql2_validation.cif.gz | 5.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ql/1ql2 ftp://data.pdbj.org/pub/pdb/validation_reports/ql/1ql2 | HTTPS FTP |
-Related structure data
Related structure data | 1ql1C 2ifnS C: citing same article (ref.) 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: 13 / Rise per n subunits: 9.15 Å / Rotation per n subunits: 197.745 °) |
-Components
#1: Protein/peptide | Mass: 4612.393 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Details: MAJOR COAT PROTEIN ASSEMBLY IN THE HIGHER-TEMPERATURE SYMMETRY Source: (gene. exp.) PSEUDOMONAS PHAGE PF1 (virus) / Description: GROWN IN PSEUDOMONAS AERUGINOSA / Production host: PSEUDOMONAS AERUGINOSA (bacteria) / References: UniProt: P03621 |
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-Experimental details
-Experiment
Experiment | Method: FIBER DIFFRACTION |
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-Sample preparation
Crystal grow | pH: 8 / Details: pH 8.00 | |||||||||||||||
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Crystal grow | *PLUS Temperature: 4 ℃ / pH: 8.1 / Method: microdialysis / Details: Nave, C., (1981) J.Mol.Biol., 149, 675. | |||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 283 K |
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Diffraction source | Source: SYNCHROTRON / Site: SRS / Beamline: PX7.2 / Wavelength: 1.488 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Details: MIRRORS |
Radiation | Monochromator: GE(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.488 Å / Relative weight: 1 |
Reflection | Resolution: 3.1→50 Å / Num. obs: 816 / % possible obs: 100 % |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2IFN Resolution: 3.1→50 Å / σ(F): 0 Details: THE MODEL WAS DERIVED FROM PDB ENTRY 2IFN, REFERENCE 1. THIS MODEL WAS REFINED AGAINST NEW FIBER DIFFRACTION DATA. THE TEMPERATURE FACTORS OF ENTRY 4IFM WERE USED WITHOUT FURTHER REFINEMENT.
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Refinement step | Cycle: LAST / Resolution: 3.1→50 Å
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Refine LS restraints |
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Software | *PLUS Name: FXPLOR / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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