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Open data
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Basic information
Entry | Database: PDB / ID: 1hgv | ||||||
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Title | Filamentous Bacteriophage PH75 | ||||||
![]() | PH75 INOVIRUS MAJOR COAT PROTEIN | ||||||
![]() | VIRUS / VIRUS COAT PROTEIN / HELICAL VIRUS COAT PROTEIN / SSDNA VIRUSES / INOVIRUS / FILAMENTOUS BACTERIOPHAGE / THERMOPHILES / MEMBRANE PROTEINS / ICOSAHEDRAL VIRUS | ||||||
Function / homology | Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #80 / Bacteriophage M13, G8P, capsid domain superfamily / helical viral capsid / host cell membrane / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Up-down Bundle / Mainly Alpha / membrane / Capsid protein G8P![]() | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Pederson, D.M. / Welsh, L.C. / Marvin, D.A. / Sampson, M. / Perham, R.N. / Yu, M. / Slater, M.R. | ||||||
![]() | ![]() Title: The Protein Capsid of Filamentous Bacteriophage Ph75 from Thermus Thermophilus Authors: Pederson, D.M. / Welsh, L.C. / Marvin, D.A. / Sampson, M. / Perham, R.N. / Yu, M. / Slater, M.R. #1: ![]() 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. #2: ![]() 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. #3: ![]() 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. #4: ![]() Title: Model-Building Studies of Inovirus: Genetic Variations on a Geometric Theme 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). 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. |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 27.1 KB | Display | ![]() |
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PDB format | ![]() | 17.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 339.4 KB | Display | ![]() |
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Full document | ![]() | 344.4 KB | Display | |
Data in XML | ![]() | 2.9 KB | Display | |
Data in CIF | ![]() | 3.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1hgzC ![]() 1hh0C ![]() 1ifnS C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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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: 66.667 °) |
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Components
#1: Protein/peptide | Mass: 4816.578 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: MAJOR COAT PROTEIN ASSEMBLY / Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Description: THE DATA IS DERIVED FROM CONTINUOUS TRANSFORM DATA AND THEREFORE THE NUMBER OF UNIQUE REFLECTIONS IS A MEANINGLESS NUMBER. |
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Crystal grow | pH: 7.5 / Details: pH 7.50 |
Crystal grow | *PLUS Method: unknown |
-Data collection
Diffraction | Mean temperature: 300 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Feb 15, 1999 / Details: MIRRORS |
Radiation | Monochromator: GE CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.488 Å / Relative weight: 1 |
Reflection | Resolution: 2.4→50 Å / % possible obs: 100 % |
Reflection | *PLUS % possible obs: 100 % |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1IFN Resolution: 2.4→50 Å / σ(F): 0 Details: THE MODEL WAS DERIVED FROM PDB ENTRY 1IFN, REFERENCE 1, BY MOLECULAR REPLACEMENT
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Refinement step | Cycle: LAST / Resolution: 2.4→50 Å
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Refine LS restraints |
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Software | *PLUS Name: FXPLOR / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Rfactor obs: 0.19 / Rfactor Rfree: 0.4 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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