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Open data
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Basic information
Entry | Database: PDB / ID: 1avy | ||||||
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Title | FIBRITIN DELETION MUTANT M (BACTERIOPHAGE T4) | ||||||
![]() | FIBRITIN | ||||||
![]() | COILED COIL / BACTERIOPHAGE T4 / STRUCTURAL PROTEIN / CHAPERONE / BACTERIOPHAGE ASSEMBLY / PROTEIN FOLDING | ||||||
Function / homology | 6-Phosphogluconate Dehydrogenase, domain 3 / Fibritin C-terminal / Fibritin C-terminal region / virion component / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Up-down Bundle / Mainly Alpha / Fibritin![]() | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Strelkov, S.V. / Tao, Y. / Mesyanzhinov, V.V. / Rossmann, M.G. | ||||||
![]() | ![]() Title: Structure of bacteriophage T4 fibritin M: a troublesome packing arrangement. Authors: Strelkov, S.V. / Tao, Y. / Shneider, M.M. / Mesyanzhinov, V.V. / Rossmann, M.G. #1: ![]() Title: Structure of Bacteriophage T4 Fibritin: A Segmented Coiled Coil and the Role of the C-Terminal Domain Authors: Tao, Y. / Strelkov, S.V. / Mesyanzhinov, V.V. / Rossmann, M.G. #2: ![]() Title: Preliminary Crystallographic Studies of Bacteriophage T4 Fibritin Confirm a Trimeric Coiled-Coil Structure Authors: Strelkov, S.V. / Tao, Y. / Rossmann, M.G. / Kurochkina, L.P. / Shneider, M.M. / Mesyanzhinov, V.V. #3: ![]() Title: Fibritin Encoded by Bacteriophage T4 Gene Wac Has a Parallel Triple-Stranded Alpha-Helical Coiled-Coil Structure Authors: Efimov, V.P. / Nepluev, I.V. / Sobolev, B.N. / Zurabishvili, T.G. / Schulthess, T. / Lustig, A. / Engel, J. / Haener, M. / Aebi, U. / Venyaminov, S.Yu. / Potekhin, S.A. / Mesyanzhinov, V.V. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 54.7 KB | Display | ![]() |
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PDB format | ![]() | 40.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 448.2 KB | Display | ![]() |
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Full document | ![]() | 454.6 KB | Display | |
Data in XML | ![]() | 13.3 KB | Display | |
Data in CIF | ![]() | 19.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1aa0S 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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Components on special symmetry positions |
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Components
#1: Protein | Mass: 7981.825 Da / Num. of mol.: 3 Fragment: DELETION MUTANT M, RESIDUES 413 - 486 OF THE WILD TYPE Mutation: R416S, S421K, N425I, N428D, T433R Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.18 Å3/Da / Density % sol: 45 % | ||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Method: vapor diffusion, hanging drop / pH: 7.5 Details: HANGING DROPS WITH 20MG/ML PROTEIN AND 1.75M LI2SO4, 0.1M TRIS-HCL, PH7.5, AS PRECIPITANT, vapor diffusion - hanging drop | ||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() |
Detector | Type: RIGAKU RAXIS IIC / Detector: IMAGE PLATE / Date: Sep 1, 1995 / Details: MIRRORS |
Radiation | Monochromator: NI FILTER / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.85→23 Å / Num. obs: 14861 / % possible obs: 89.8 % / Observed criterion σ(I): 0 / Redundancy: 2.7 % / Biso Wilson estimate: 20.9 Å2 / Rsym value: 0.036 |
Reflection shell | Resolution: 1.85→1.91 Å / Rsym value: 0.182 / % possible all: 53.6 |
Reflection | *PLUS Num. measured all: 39783 / Rmerge(I) obs: 0.036 |
Reflection shell | *PLUS % possible obs: 53.6 % / Rmerge(I) obs: 0.182 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1AA0 Resolution: 1.85→23 Å / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 Details: BULK SOLVENT WAS MODELED USING A STANDARD X-PLOR PROCEDURE, WITH BULK SOLVENT DENSITY 0.432 E/A3.
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Displacement parameters | Biso mean: 32.81 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.85→23 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.85→1.93 Å / Rfactor Rfree: 0.416 / Rfactor Rwork: 0.317 / Total num. of bins used: 10 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Xplor file |
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Software | *PLUS Name: ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor obs: 0.317 |