+Open data
-Basic information
Entry | Database: PDB / ID: 3r4a | ||||||
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Title | Crystal structure of the 4-helix coiled coil CC-tet | ||||||
Components | coiled coil helix CC-tet | ||||||
Keywords | DE NOVO PROTEIN / coiled coil domain / tetramer / KIH interactions / synthetic biology | ||||||
Biological species | Synthetic construct (others) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.0701 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 | 3r4a.cif.gz | 31.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3r4a.ent.gz | 23.1 KB | Display | PDB format |
PDBx/mmJSON format | 3r4a.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3r4a_validation.pdf.gz | 446 KB | Display | wwPDB validaton report |
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Full document | 3r4a_full_validation.pdf.gz | 446.8 KB | Display | |
Data in XML | 3r4a_validation.xml.gz | 6.9 KB | Display | |
Data in CIF | 3r4a_validation.cif.gz | 8.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/r4/3r4a ftp://data.pdbj.org/pub/pdb/validation_reports/r4/3r4a | HTTPS FTP |
-Related structure data
Related structure data | 3r3kC 3r46C 3r47C 3r48C 3r4hSC 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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Details | TETRAMER CONFIRMED BY ANALYTICAL ULTRACENTRIFUGATION |
-Components
#1: Protein/peptide | Mass: 3363.000 Da / Num. of mol.: 4 / Source method: obtained synthetically Details: Peptide synthesis was carried out according to standard Fmoc SPPS protocols 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: 2.18 Å3/Da / Density % sol: 43.59 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: 0.2M lithium sulfate, 0.1M Tris pH 8.5, 1.26M ammonium sulfate, supplemented with 25% glycerol for cryo-protection , VAPOR DIFFUSION, SITTING DROP, temperature 291K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I02 |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Aug 8, 2009 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Relative weight: 1 |
Reflection | Resolution: 2.07→41.03 Å / Num. obs: 7490 / % possible obs: 100 % / Redundancy: 6.7 % / Rmerge(I) obs: 0.102 / Net I/σ(I): 12.8 |
Reflection shell | Resolution: 2.07→2.18 Å / Redundancy: 6.7 % / Rmerge(I) obs: 0.624 / Mean I/σ(I) obs: 2.9 / % possible all: 99.9 |
-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3R4H WITH IODOPHENYL GROUPS CHANGED TO TYROSINE Resolution: 2.0701→22.819 Å / Occupancy max: 1 / Occupancy min: 1 / SU ML: 0.17 / σ(F): 0 / Phase error: 24.61 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.95 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 36.016 Å2 / ksol: 0.354 e/Å3 | ||||||||||||||||||||||||||||
Displacement parameters | Biso max: 70 Å2 / Biso mean: 29.7758 Å2 / Biso min: 14.43 Å2
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Refinement step | Cycle: LAST / Resolution: 2.0701→22.819 Å
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Refine LS restraints |
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LS refinement shell |
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