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Yorodumi- PDB-6atn: Exploring Cystine Dense Peptide Space to Open a Unique Molecular ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6atn | ||||||
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Title | Exploring Cystine Dense Peptide Space to Open a Unique Molecular Toolbox | ||||||
Components | Potassium channel toxin alpha-KTx 4.5 | ||||||
Keywords | TOXIN / Knottins / Cystine knot / Toxins | ||||||
Function / homology | Scorpion short toxins signature. / Scorpion short chain toxin, potassium channel inhibitor / Scorpion short toxin, BmKK2 / Knottin, scorpion toxin-like superfamily / ion channel inhibitor activity / : / toxin activity / extracellular region / Potassium channel toxin alpha-KTx 4.5 Function and homology information | ||||||
Biological species | Tityus costatus (scorpion) | ||||||
Method | X-RAY DIFFRACTION / SAD / Resolution: 1.76 Å | ||||||
Authors | Gewe, M.M. / Rupert, P. / Strong, R.K. | ||||||
Citation | Journal: Nat. Struct. Mol. Biol. / Year: 2018 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6atn.cif.gz | 17.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6atn.ent.gz | 11.4 KB | Display | PDB format |
PDBx/mmJSON format | 6atn.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/at/6atn ftp://data.pdbj.org/pub/pdb/validation_reports/at/6atn | HTTPS FTP |
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-Related structure data
Related structure data | 6atlC 6atsC 6atuC 6atwC 6au7C 6aupC 6av8C 6avaC 6avcC 6avdC 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 | Monomer as determined by gel filtration. |
-Components
#1: Protein/peptide | Mass: 4144.028 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Tityus costatus (scorpion) / Cell line (production host): HEK-293F / Production host: Homo sapiens (human) / References: UniProt: Q5G8B6 |
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#2: 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: 2.9 Å3/Da / Density % sol: 57.59 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 2.4 M Na malonate pH 7.0 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54 Å |
Detector | Type: RIGAKU SATURN 944+ / Detector: CCD / Date: Apr 4, 2016 |
Radiation | Monochromator: osmic varimax / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54 Å / Relative weight: 1 |
Reflection | Resolution: 1.76→50 Å / Num. obs: 8524 / % possible obs: 44.7 % / Redundancy: 2.1 % / Χ2: 2.1 / Net I/σ(I): 25.05 |
Reflection shell | Resolution: 1.76→1.79 Å / Redundancy: 1.1 % / Rmerge(I) obs: 0.159 / Num. unique obs: 62 / CC1/2: 0.94 / Rpim(I) all: 0.173 / % possible all: 6.4 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 1.76→32.93 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.949 / SU B: 1.829 / SU ML: 0.059 / Cross valid method: THROUGHOUT / ESU R: 0.103 / ESU R Free: 0.115 / 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: 26.843 Å2
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Refinement step | Cycle: 1 / Resolution: 1.76→32.93 Å
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Refine LS restraints |
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