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Yorodumi- PDB-6olo: Controlling the Self-Assembly of Synthetic Metal-Coordinating Coi... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6olo | ||||||
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Title | Controlling the Self-Assembly of Synthetic Metal-Coordinating Coiled-Coil Peptides: Hexagonal Lattice from a Trimeric Coiled Coil | ||||||
Components | Designed trimeric coiled coil peptide | ||||||
Keywords | DE NOVO PROTEIN / metal coordination framework / supramolecular assembly | ||||||
Function / homology | COPPER (II) ION Function and homology information | ||||||
Biological species | synthetic construct (others) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.3 Å | ||||||
Authors | Schieb, K.A. / Horne, W.S. | ||||||
Citation | Journal: Chem.Commun.(Camb.) / Year: 2019 Title: Understanding and controlling the metal-directed assembly of terpyridine-functionalized coiled-coil peptides. Authors: Scheib, K.A. / Tavenor, N.A. / Lawless, M.J. / Saxena, S. / Horne, W.S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6olo.cif.gz | 15 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6olo.ent.gz | 9.1 KB | Display | PDB format |
PDBx/mmJSON format | 6olo.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6olo_validation.pdf.gz | 406.3 KB | Display | wwPDB validaton report |
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Full document | 6olo_full_validation.pdf.gz | 406.3 KB | Display | |
Data in XML | 6olo_validation.xml.gz | 3 KB | Display | |
Data in CIF | 6olo_validation.cif.gz | 3.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ol/6olo ftp://data.pdbj.org/pub/pdb/validation_reports/ol/6olo | HTTPS FTP |
-Related structure data
Related structure data | 6olnC 4dzlS S: Starting model for refinement C: citing same article (ref.) |
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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: 3175.832 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
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#2: Chemical | ChemComp-CU / |
#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: 2.03 Å3/Da / Density % sol: 39.35 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: 0.1 M Tris pH 8.5, 25% w/v PEG 3350, 5 mM copper(II) chloride |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU FR-E SUPERBRIGHT / Wavelength: 1.5418 Å |
Detector | Type: RIGAKU SATURN 944 / Detector: CCD / Date: Jan 14, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→26.61 Å / Num. obs: 1094 / % possible obs: 100 % / Redundancy: 5.25 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 16.3 |
Reflection shell | Resolution: 2.3→2.38 Å / Redundancy: 3.76 % / Rmerge(I) obs: 0.369 / Mean I/σ(I) obs: 2.4 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4DZL, CHAIN A Resolution: 2.3→19.87 Å / SU ML: 0.26 / Cross valid method: FREE R-VALUE / σ(F): 2.19 / Phase error: 28.95
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.3→19.87 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.3011→2.38 Å
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