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Yorodumi- PDB-2oxj: Helix Bundle Quaternary Structure from alpha/beta-Peptide Foldame... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2oxj | |||||||||
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Title | Helix Bundle Quaternary Structure from alpha/beta-Peptide Foldamers: GCN4-p1 with beta-residues at b and f heptad positions. | |||||||||
Components | hybrid alpha/beta peptide based on the GCN4-p1 sequence; heptad positions b and f substituted with beta-amino acids | |||||||||
Keywords | UNKNOWN FUNCTION / helix bundle / foldamer | |||||||||
Function / homology | ACETATE ION Function and homology information | |||||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2 Å | |||||||||
Authors | Horne, W.S. / Price, J.L. / Keck, J.L. / Gellman, S.H. | |||||||||
Citation | Journal: J.Am.Chem.Soc. / Year: 2007 Title: Helix Bundle Quaternary Structure from alpha/beta-Peptide Foldamers. Authors: Horne, W.S. / Price, J.L. / Keck, J.L. / 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 | 2oxj.cif.gz | 57.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2oxj.ent.gz | 47.5 KB | Display | PDB format |
PDBx/mmJSON format | 2oxj.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2oxj_validation.pdf.gz | 478.5 KB | Display | wwPDB validaton report |
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Full document | 2oxj_full_validation.pdf.gz | 487.9 KB | Display | |
Data in XML | 2oxj_validation.xml.gz | 10.2 KB | Display | |
Data in CIF | 2oxj_validation.cif.gz | 12.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ox/2oxj ftp://data.pdbj.org/pub/pdb/validation_reports/ox/2oxj | HTTPS FTP |
-Related 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: 4155.923 Da / Num. of mol.: 3 / Source method: obtained synthetically / Details: synthetic peptide #2: Chemical | ChemComp-ACT / | #3: 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: 1.81 Å3/Da / Density % sol: 31.96 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: 0.2 M sodium acetate, 0.1 M Tris hydrochloride, 30% w/v PEG 4000, pH 8.5, 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: Aug 31, 2006 / 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→37.6 Å / Num. all: 6503 / Num. obs: 6503 / % possible obs: 99.5 % / Redundancy: 6.2 % / Rsym value: 4.5 / Net I/σ(I): 21.6 |
Reflection shell | Resolution: 2→2.1 Å / Redundancy: 2.7 % / Mean I/σ(I) obs: 3.6 / Rsym value: 29.8 / % possible all: 98.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→25 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.919 / SU B: 6.005 / SU ML: 0.167 / Cross valid method: THROUGHOUT / ESU R: 0.262 / ESU R Free: 0.22 / 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: 1.4 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 19.565 Å2
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Refinement step | Cycle: LAST / Resolution: 2→25 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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