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Yorodumi- PDB-3hey: Cyclic residues in alpha/beta-peptide helix bundles: GCN4-pLI sid... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3hey | |||||||||
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Title | Cyclic residues in alpha/beta-peptide helix bundles: GCN4-pLI side chain sequence on an (alpha-alpha-beta) backbone with cyclic beta-residues at positions 1, 4, 10, 19 and 28 | |||||||||
Components | alpha/beta-peptide based on the GCN4-pLI side chain sequence with an (alpha-alpha-beta) backbone and cyclic beta-residues at positions 1, 4, 10, 19 and 28 | |||||||||
Keywords | DE NOVO PROTEIN / helix bundle / foldamer / alpha/beta-peptide | |||||||||
Function / homology | ACETATE ION Function and homology information | |||||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2 Å | |||||||||
Authors | Horne, W.S. / Price, J.L. / Gellman, S.H. | |||||||||
Citation | Journal: J.Am.Chem.Soc. / Year: 2010 Title: Structural consequences of beta-amino acid preorganization in a self-assembling alpha/beta-peptide: fundamental studies of foldameric helix bundles. Authors: Price, J.L. / 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 | 3hey.cif.gz | 27.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3hey.ent.gz | 19.8 KB | Display | PDB format |
PDBx/mmJSON format | 3hey.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3hey_validation.pdf.gz | 436.7 KB | Display | wwPDB validaton report |
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Full document | 3hey_full_validation.pdf.gz | 439.9 KB | Display | |
Data in XML | 3hey_validation.xml.gz | 5.4 KB | Display | |
Data in CIF | 3hey_validation.cif.gz | 6.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/he/3hey ftp://data.pdbj.org/pub/pdb/validation_reports/he/3hey | HTTPS FTP |
-Related structure data
Related structure data | 3hetC 3heuC 3hevSC 3hewC 3hexC 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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Unit cell |
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-Components
#1: Protein/peptide | Mass: 4056.900 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: Synthetic peptide |
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#2: Chemical | ChemComp-ACT / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.11 Å3/Da / Density % sol: 41.84 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4.6 Details: 0.3 M sodium acetate pH 4.6, 0.25 magnesium formate, 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: Mar 10, 2008 / 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→23.48 Å / Num. obs: 2612 / % possible obs: 99.3 % / Redundancy: 9.2 % / Rsym value: 0.046 / Net I/σ(I): 29.5 |
Reflection shell | Resolution: 2→2.1 Å / Redundancy: 3.2 % / Mean I/σ(I) obs: 5.2 / Rsym value: 0.203 / % possible all: 94.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3HEV Resolution: 2→23.48 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.904 / SU B: 4.317 / SU ML: 0.117 / Cross valid method: THROUGHOUT / ESU R: 0.209 / ESU R Free: 0.185 / 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: 14.569 Å2
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Refinement step | Cycle: LAST / Resolution: 2→23.48 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2→2.052 Å / Total num. of bins used: 20
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