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Yorodumi- PDB-1ifd: MODEL-BUILDING STUDIES OF INOVIRUS: GENETIC VARIATIONS ON A GEOME... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1ifd | ||||||
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Title | MODEL-BUILDING STUDIES OF INOVIRUS: GENETIC VARIATIONS ON A GEOMETRIC THEME | ||||||
Components | INOVIRUSFf phages | ||||||
Keywords | VIRUS / Helical virus | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Enterobacteria phage fd (virus) | ||||||
Method | FIBER DIFFRACTION / Resolution: 4 Å | ||||||
Authors | Marvin, D.A. | ||||||
Citation | Journal: Int.J.Biol.Macromol. / Year: 1990 Title: Model-building studies of Inovirus: genetic variations on a geometric theme. Authors: Marvin, D.A. #1: Journal: Int.J.Biol.Macromol. / Year: 1989 Title: Dynamics of Telescoping Inovirus: A Mechanism for Assembly at Membrane Adhesions Authors: Marvin, D.A. #3: Journal: Structural Molecular Biology / Year: 1982 Title: X-Ray Fiber Diffraction Authors: Marvin, D.A. / Nave, C. #4: Journal: Nature / Year: 1981 Title: Structure of the Protein and DNA in Fd Filamentous Bacterial Virus Authors: Banner, D.W. / Nave, C. / Marvin, D.A. #5: Journal: J.Mol.Biol. / Year: 1974 Title: Filamentous Bacterial Viruses Xii. Molecular Architecture of the Class I (Fd, If1, Ike) Virion Authors: Marvin, D.A. / Pigram, W.J. / Wiseman, R.L. / Wachtel, E.J. / Marvin, F.J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1ifd.cif.gz | 20.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1ifd.ent.gz | 13.1 KB | Display | PDB format |
PDBx/mmJSON format | 1ifd.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/if/1ifd ftp://data.pdbj.org/pub/pdb/validation_reports/if/1ifd | HTTPS FTP |
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-Related 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: 5 / Dyad axis: no / N subunits divisor: 1 / Num. of operations: 55 / Rise per n subunits: 16 Å / Rotation per n subunits: -33.23 °) |
-Components
#1: Protein/peptide | Mass: 5244.000 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Enterobacteria phage fd (virus) / Genus: InovirusFf phages / Species: Enterobacteria phage M13 / Plasmid: M13 / References: UniProt: P69539 |
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Source details | INOVIRUS STRAIN FD WAS GROWN IN ESCHERICHIA COLI. THERE ARE TWO SYMMETRY CLASSES OF INOVIRUS. CLASS ...INOVIRUS STRAIN FD WAS GROWN IN ESCHERICHI |
-Experimental details
-Experiment
Experiment | Method: FIBER DIFFRACTION |
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-Sample preparation
Crystal grow | *PLUS Method: fibre diffraction |
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-Data collection
Radiation wavelength | Relative weight: 1 |
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-Processing
Software | Name: EREF / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Refinement | Highest resolution: 4 Å Details: THE MODEL OF THE VIRION HELIX ASYMMETRIC UNIT IS AN ALPHA-HELIX APPROXIMATION TO THE STRUCTURE, SO THE ENTIRE MODEL IS ONE STRETCH OF GENTLY-CURVED HELIX. COORDINATES ARE GIVEN FOR A SINGLE ...Details: THE MODEL OF THE VIRION HELIX ASYMMETRIC UNIT IS AN ALPHA-HELIX APPROXIMATION TO THE STRUCTURE, SO THE ENTIRE MODEL IS ONE STRETCH OF GENTLY-CURVED HELIX. COORDINATES ARE GIVEN FOR A SINGLE ASYMMETRIC UNIT OF THE COAT PROTEIN ASSEMBLY. THE COMPLETE PROTEIN ASSEMBLY CONTAINS SEVERAL THOUSAND ASYMMETRIC UNITS; THE EXACT NUMBER DEPENDS ON THE LENGTH OF THE DNA. THE PROTEIN ASSEMBLY FORMS A CYLINDRICAL SHELL SURROUNDING A DNA CORE. THE DNA IS ABOUT 12% BY WEIGHT OF THE FD VIRION, AND PROBABLY HAS NO WELL-DEFINED STRUCTURE OTHER THAN THAT IMPOSED BY ITS SINGLE-STRANDED CIRCULAR TOPOLOGY: TWO OPPOSITELY DIRECTED DNA CHAINS RUN ALONG THE LENGTH OF THE VIRION TO COMPLETE THE CIRCLE. THE DNA MAY BE A LEFT-HANDED HELIX (SEE JRNL REFERENCE). THE TWO ENDS OF THE VIRION ARE CAPPED BY A FEW COPIES OF MINOR COAT PROTEINS, WHOSE STRUCTURE IS NOT KNOWN. THESE PROTEINS INTERACT WITH THE ENDS OF THE MAJOR COAT PROTEIN ASSEMBLY. THE N-TERMINAL END OF INOVIRUS HAS AN OPEN CUP SHAPE, AND THE C-TERMINAL END IS THE COMPLEMENT OF THIS, A POINTED ARROWHEAD SHAPE (SEE REFERENCES 1 AND 2). THE TWO ENDS OF THE FD ASSEMBLY CAN BE GENERATED BY OPERATING REPEATEDLY (SAY 10 - 20 TIMES) ON THE HELIX UNIT CELL CONTENTS (THE GROUP OF 5 ASYMMETRIC UNITS) WITH THE HELIX PARAMETERS, GIVING TWO DIFFERENT ENDS CONNECTED BY A SHORT SHAFT. SINCE THE MAJOR COAT PROTEIN SUBUNITS AT THE ENDS HAVE FEWER NEIGHBORS THAN THOSE IN THE CENTER OF THE ASSEMBLY, THEIR CONFORMATIONS ARE LESS CONSTRAINED AND MAY BE MODIFIED BY INTERACTION WITH THE MINOR COAT PROTEINS. THE HELIX UNIT CELL PARAMETERS ARE AFFECTED BY EXPERIMENTAL CONDITIONS SUCH AS HYDRATION, PH AND TEMPERATURE. BECAUSE OF THE OVERLAPPING INTERDIGITATED NATURE OF THE ASSEMBLY, EVEN SMALL CHANGES IN THE UNIT CELL PARAMETERS ARE ACCOMPANIED BY CHANGES IN THE SHAPE OF THE ASYMMETRIC UNIT. THESE CHANGES DO NOT ALTER THE PATTERN OF SIDE CHAIN INTERLOCKING BETWEEN NEIGHBORING ASYMMETRIC UNITS, BUT THEY CAN ALTER LOCAL NON-BONDED CONTACTS BY SEVERAL TENTHS OF AN ANGSTROM. THE DEPOSITORS DEFINE A CANONICAL HELIX UNIT CELL WITH PARAMETERS T = -33.23 DEGREES, P = 16.0 ANGSTROMS AND GIVE THE ATOMIC COORDINATES FOR THE ASYMMETRIC UNIT IN THIS UNIT CELL. TO DETERMINE THE COORDINATES OF THE ASYMMETRIC UNIT IN A NEW UNIT CELL WITH SLIGHTLY DIFFERENT PARAMETERS (T', P'), CONVERT FROM CARTESIAN COORDINATES TO CYLINDRICAL-POLAR COORDINATES AND USE EQUATION 5 OF THE JRNL REFERENCE. AN EQUIVALENT ALTERNATIVE METHOD IS TO APPLY A VARIABLE MATRIX THAT IS A FUNCTION OF THE Z COORDINATE OF THE ATOMS. DEFINE A SLEW COEFFICIENT S=(T'-T)/P; FOR EXAMPLE, FOR FD AT PH 2, T'=-36.0 DEGREES DEGREES, P'=16.15 ANGSTROMS AND S=-0.173 DEGREE/ANGSTROM. THEN, TO GENERATE THE SLEWED COORDINATES, APPLY THE MATRIX AND VECTOR (RECALCULATED FOR EACH ATOM): | COS(S*Z) -SIN(S*Z) 0 | | 0 | | SIN(S*Z) COS(S*Z) 0 | + | 0 | | 0 0 1 | | (P'/P)*Z | SLEWING THE COORDINATES IN THIS WAY GIVES RISE TO SMALL LOCAL DISTORTIONS IN COVALENT BOND LENGTHS AND BOND ANGLES, WHICH CAN BE CORRECTED BY A FEW CYCLES OF ENERGY MINIMIZATION. THE TEMPERATURE FACTOR WAS NOT REFINED AND IS GIVEN THE ARBITRARY VALUE OF 10. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Highest resolution: 4 Å
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Refine LS restraints |
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