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- PDB-3f87: An alpha/beta-Peptide Helix Bundle with a Pure beta-Amino Acid Co... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3f87 | |||||||||
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Title | An alpha/beta-Peptide Helix Bundle with a Pure beta-Amino Acid Core and a Distinctive Quarternary Structure: GCN4pLI derivative with beta residues at a and d heptad positions - higher symmetry crystal | |||||||||
![]() | GCN4pLI-betaAD | |||||||||
![]() | UNKNOWN FUNCTION / alpha/beta-peptide / helix bundle / foldamer / GCN4 derivative | |||||||||
Function / homology | IODIDE ION![]() | |||||||||
Method | ![]() ![]() | |||||||||
![]() | Giuliano, M.W. / Horne, W.S. / Gellman, S.H. | |||||||||
![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 73.6 KB | Display | ![]() |
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PDB format | ![]() | 64.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 471.2 KB | Display | ![]() |
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Full document | ![]() | 486.3 KB | Display | |
Data in XML | ![]() | 11.9 KB | Display | |
Data in CIF | ![]() | 14.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related 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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Unit cell |
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Details | The asymmetric unit contains half of two separate, NCS-related tetrameric helix bundles: The second half of the first tetramer, which contains chains A and B, is generated by: (-y, -x, -z+1/2) + (010) / The asymmetric unit contains half of two separate, NCS-related tetrameric helix bundles: The second half of the second tetramer, which contains chains C and D, is generated by: (y, x, -z) + (100) |
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Components
#1: Protein/peptide | Mass: 4212.099 Da / Num. of mol.: 4 / Source method: obtained synthetically / Details: Synthetic Peptide / References: ![]() #2: Chemical | ChemComp-IOD / #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.68 Å3/Da / Density % sol: 66.54 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 0.12 M NaI, 0.08 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: ![]() |
Detector | Type: BRUKER SMART 6000 / Detector: CCD / Date: Jun 21, 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: 2.4→50.4 Å / Num. all: 10451 / Num. obs: 10316 / % possible obs: 98.7 % / Redundancy: 12.61 % / Rmerge(I) obs: 0.148 / Rsym value: 0.061 |
Reflection shell | Resolution: 2.4→2.49 Å / Redundancy: 9.76 % / Rmerge(I) obs: 0.521 / Mean I/σ(I) obs: 4.41 / Num. unique all: 1096 / Rsym value: 0.228 / % possible all: 99.5 |
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Processing
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Refinement | Method to determine structure: ![]()
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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: 17.868 Å2
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Refinement step | Cycle: LAST / Resolution: 2.4→50.4 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.396→2.458 Å / Total num. of bins used: 20
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