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- PDB-6ava: Exploring Cystine Dense Peptide Space to Open a Unique Molecular ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6ava | ||||||
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Title | Exploring Cystine Dense Peptide Space to Open a Unique Molecular Toolbox | ||||||
![]() | Insectotoxin-I1 | ||||||
![]() | TOXIN / Knottins / Cystine knot / Toxins | ||||||
Function / homology | Scorpion short chain toxin, chloride channel inhibitor / Scorpion short toxin / Scorpion short toxin chloride channel inhibitor subfamily profile. / Knottin, scorpion toxin-like superfamily / : / toxin activity / extracellular region / Insectotoxin-I1![]() | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Gewe, M.M. / Rupert, P. / Strong, R.K. | ||||||
![]() | ![]() Title: Screening, large-scale production and structure-based classification of cystine-dense peptides. Authors: Correnti, C.E. / Gewe, M.M. / Mehlin, C. / Bandaranayake, A.D. / Johnsen, W.A. / Rupert, P.B. / Brusniak, M.Y. / Clarke, M. / Burke, S.E. / De Van Der Schueren, W. / Pilat, K. / Turnbaugh, S. ...Authors: Correnti, C.E. / Gewe, M.M. / Mehlin, C. / Bandaranayake, A.D. / Johnsen, W.A. / Rupert, P.B. / Brusniak, M.Y. / Clarke, M. / Burke, S.E. / De Van Der Schueren, W. / Pilat, K. / Turnbaugh, S.M. / May, D. / Watson, A. / Chan, M.K. / Bahl, C.D. / Olson, J.M. / Strong, R.K. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 42 KB | Display | ![]() |
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PDB format | ![]() | 29.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 6atlC ![]() 6atnC ![]() 6atsC ![]() 6atuC ![]() 6atwC ![]() 6au7C ![]() 6aupC ![]() 6av8C ![]() 6avcC ![]() 6avdC ![]() 1sisS C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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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: 4159.971 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Cell line (production host): HEK-293F / Production host: ![]() #2: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.27 Å3/Da / Density % sol: 45.88 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 4.5 / Details: 100 mM Na Acetate pH 4.5, 600 mM AmPO4 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() |
Detector | Type: RIGAKU SATURN 944 / Detector: CCD / Date: Jul 2, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→50 Å / Num. obs: 4317 / % possible obs: 100 % / Redundancy: 58.4 % / Rmerge(I) obs: 0.124 / Rpim(I) all: 0.021 / Net I/σ(I): 44.9 |
Reflection shell | Resolution: 2.2→2.26 Å / Redundancy: 59.5 % / Rmerge(I) obs: 0.348 / Mean I/σ(I) obs: 26.7 / Num. unique obs: 409 / CC1/2: 0.993 / Rpim(I) all: 0.049 / Χ2: 2.488 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1SIS Resolution: 2.2→37.5 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.928 / SU B: 7.766 / SU ML: 0.11 / Cross valid method: THROUGHOUT / ESU R: 0.249 / ESU R Free: 0.209 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 15.807 Å2
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Refinement step | Cycle: 1 / Resolution: 2.2→37.5 Å
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Refine LS restraints |
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