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Yorodumi- PDB-3f86: An alpha/beta-Peptide Helix Bundle with a Pure beta-Amino Acid Co... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3f86 | |||||||||
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Title | An alpha/beta-Peptide Helix Bundle with a Pure beta-Amino Acid Core and a Distinctive Quaternary Structure: GCN4pLI derivative with beta residues at a and d heptad positions | |||||||||
Components | GCN4pLI-betaAD | |||||||||
Keywords | UNKNOWN FUNCTION / alpha/beta-peptide / helix bundle / foldamer / coiled coil / GCN4 derivative | |||||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2 Å | |||||||||
Authors | Giuliano, M.W. / Horne, W.S. / Gellman, S.H. | |||||||||
Citation | Journal: J.Am.Chem.Soc. / Year: 2009 Title: An alpha/beta-peptide helix bundle with a pure beta3-amino acid core and a distinctive quaternary structure. Authors: Giuliano, M.W. / Horne, W.S. / Gellman, S.H. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3f86.cif.gz | 124.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3f86.ent.gz | 112.5 KB | Display | PDB format |
PDBx/mmJSON format | 3f86.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3f86_validation.pdf.gz | 506.7 KB | Display | wwPDB validaton report |
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Full document | 3f86_full_validation.pdf.gz | 531.5 KB | Display | |
Data in XML | 3f86_validation.xml.gz | 17.9 KB | Display | |
Data in CIF | 3f86_validation.cif.gz | 23.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/f8/3f86 ftp://data.pdbj.org/pub/pdb/validation_reports/f8/3f86 | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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Details | The asymmetric unit of the structure contains two helix bundle tetramers ('biological' units): The first tetramer is composed of chains A, B, C, and D. / The asymmetric unit of the structure contains two helix bundle tetramers ('biological' units): The second tetramer is composed of chains E, F, G, and H. |
-Components
#1: Protein/peptide | Mass: 4212.099 Da / Num. of mol.: 8 / Source method: obtained synthetically / Details: Synthetic Peptide #2: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 1.93 Å3/Da / Density % sol: 36.31 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 0.2 M NaCl, 0.1 M HEPES-Na pH 7.5, 20% (v/v) 2-methyl-2,4-pentanediol (MPD) , VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: BRUKER AXS MICROSTAR / Wavelength: 1.5418 Å |
Detector | Type: BRUKER SMART 6000 / Detector: CCD / Date: May 28, 2007 / Details: confocal mirrors |
Radiation | Monochromator: Gobel mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2→47.4 Å / Num. all: 16772 / Num. obs: 16551 / % possible obs: 98.7 % / Redundancy: 5.91 % / Rmerge(I) obs: 0.055 / Rsym value: 0.0352 |
Reflection shell | Resolution: 2→2.1 Å / Redundancy: 2.27 % / Rmerge(I) obs: 0.173 / Mean I/σ(I) obs: 4.2 / Num. unique all: 2119 / Rsym value: 0.267 / % possible all: 92.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→47.4 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.937 / Cross valid method: THROUGHOUT / ESU R: 0.257 / ESU R Free: 0.213 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 19.611 Å2
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Refinement step | Cycle: LAST / Resolution: 2→47.4 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.999→2.051 Å / Total num. of bins used: 20
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