+Open data
-Basic information
Entry | Database: PDB / ID: 3r3k | ||||||
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Title | Crystal structure of a parallel 6-helix coiled coil | ||||||
Components | CChex-Phi22 helix | ||||||
Keywords | DE NOVO PROTEIN / parallel hexamer / KIH interactions / hydrophobic channel / synthetic biology | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.2009 Å | ||||||
Authors | Zaccai, N.R. / Chi, B.H.C. / Woolfson, D.N. / Brady, R.L. | ||||||
Citation | Journal: Nat.Chem.Biol. / Year: 2011 Title: A de novo peptide hexamer with a mutable channel. Authors: Zaccai, N.R. / Chi, B. / Thomson, A.R. / Boyle, A.L. / Bartlett, G.J. / Bruning, M. / Linden, N. / Sessions, R.B. / Booth, P.J. / 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 | 3r3k.cif.gz | 27.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3r3k.ent.gz | 22.2 KB | Display | PDB format |
PDBx/mmJSON format | 3r3k.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3r3k_validation.pdf.gz | 460.4 KB | Display | wwPDB validaton report |
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Full document | 3r3k_full_validation.pdf.gz | 462.9 KB | Display | |
Data in XML | 3r3k_validation.xml.gz | 7.7 KB | Display | |
Data in CIF | 3r3k_validation.cif.gz | 9.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/r3/3r3k ftp://data.pdbj.org/pub/pdb/validation_reports/r3/3r3k | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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2 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein/peptide | Mass: 3477.891 Da / Num. of mol.: 3 / Fragment: helix from coiled coil domain / Source method: obtained synthetically Details: Peptide synthesis carried out according to standard Fmoc SPPS protocols #2: Chemical | #3: Chemical | ChemComp-NA / #4: Chemical | #5: 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: 2.67 Å3/Da / Density % sol: 53.94 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 20 mM sodium L-glutamate, 20 mM alanine (racemic), 20 mM glycine, 20 mM lysine hydrochloride (racemic), 20 mM serine (racemic), 50 mM sodium HEPES, 50 mM MOPS (acid) pH 7.5, 20 % ethylene ...Details: 20 mM sodium L-glutamate, 20 mM alanine (racemic), 20 mM glycine, 20 mM lysine hydrochloride (racemic), 20 mM serine (racemic), 50 mM sodium HEPES, 50 mM MOPS (acid) pH 7.5, 20 % ethylene glycol,10 % PEG 8K, VAPOR DIFFUSION, SITTING DROP, temperature 291K |
-Data collection
Diffraction | Mean temperature: 200 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 1.7 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: May 17, 2010 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.7 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→50.14 Å / Num. obs: 5716 / % possible obs: 95.6 % / Redundancy: 5.7 % / Rmerge(I) obs: 0.109 / Net I/σ(I): 9.3 |
Reflection shell | Resolution: 2.2→2.32 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.339 / Mean I/σ(I) obs: 2.2 / % possible all: 72.1 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 2.2009→23.21 Å / SU ML: 0.25 / σ(F): 0 / Phase error: 24.86 / Stereochemistry target values: ML Details: F(+) and F(-) treated separately during refinement.
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 61.818 Å2 / ksol: 0.406 e/Å3 | ||||||||||||||||||||||||||||
Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 2.2009→23.21 Å
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Refine LS restraints |
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LS refinement shell |
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