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Yorodumi- PDB-4h8l: Crystal structure of a parallel 6-helix coiled coil CC-Hex-D24-A5/7C -
+Open data
-Basic information
Entry | Database: PDB / ID: 4h8l | ||||||
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Title | Crystal structure of a parallel 6-helix coiled coil CC-Hex-D24-A5/7C | ||||||
Components | CC-Hex-D24-A5/7C | ||||||
Keywords | DE NOVO PROTEIN / CC-Hex / hexameric coiled coil / parallel / N-terminal acetylation / C-terminal amidation | ||||||
Biological species | Synthetic construct (others) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7501 Å | ||||||
Authors | Chi, B. / Zaccai, N.R. / Brady, R.L. / Woolfson, D.N. | ||||||
Citation | Journal: J.Am.Chem.Soc. Title: TBA Authors: Chi, B. / Zaccai, N.R. / Brady, R.L. / Woolfson, D.N. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4h8l.cif.gz | 41.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4h8l.ent.gz | 31.7 KB | Display | PDB format |
PDBx/mmJSON format | 4h8l.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4h8l_validation.pdf.gz | 471.6 KB | Display | wwPDB validaton report |
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Full document | 4h8l_full_validation.pdf.gz | 474.4 KB | Display | |
Data in XML | 4h8l_validation.xml.gz | 9.3 KB | Display | |
Data in CIF | 4h8l_validation.cif.gz | 12.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/h8/4h8l ftp://data.pdbj.org/pub/pdb/validation_reports/h8/4h8l | HTTPS FTP |
-Related structure data
Related structure data | 3r46S S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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Unit cell |
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Components on special symmetry positions |
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Details | Self-assembling. Disulfides form under redox conditions, Cys 5 - Cys 7' inter-chain linkage |
-Components
#1: Protein/peptide | Mass: 3429.061 Da / Num. of mol.: 6 / Source method: obtained synthetically / Details: standard F-moc solid phase peptide synthesis / Source: (synth.) Synthetic construct (others) #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: 2.05 Å3/Da / Density % sol: 39.89 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: 30 mM sodium nitrate, 30 mM disodium hydrogen phosphate, 30 mM ammonium sulfate, 100 mM bicine/Trizma base pH 8.5, 12.5 % PEG 1K, 12.5 % PEG 3350, 12.5 % MPD, VAPOR DIFFUSION, SITTING DROP, temperature 291K |
-Data collection
Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.97 Å |
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Detector | Type: ADSC QUANTUM 315 / Detector: CCD |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97 Å / Relative weight: 1 |
Reflection | Resolution: 1.75→36.4 Å / Num. all: 17439 / Num. obs: 16619 |
-Processing
Software | Name: PHENIX / Version: (phenix.refine: 1.7_650) / Classification: refinement | |||||||||||||||||||||||||||||||||||||||||||||||||
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3R46 Resolution: 1.7501→30.031 Å / SU ML: 0.21 / σ(F): 0 / Phase error: 25.48 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.72 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 80 Å2 / ksol: 0.423 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 1.7501→30.031 Å
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Refine LS restraints |
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LS refinement shell |
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