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Yorodumi- PDB-6atw: Exploring Cystine Dense Peptide Space to Open a Unique Molecular ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6atw | ||||||
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Title | Exploring Cystine Dense Peptide Space to Open a Unique Molecular Toolbox | ||||||
Components | Chlorotoxin | ||||||
Keywords | 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. / peptidase inhibitor activity / Knottin, scorpion toxin-like superfamily / chloride channel regulator activity / toxin activity / extracellular region / Chlorotoxin Function and homology information | ||||||
Biological species | Leiurus quinquestriatus quinquestriatus (Egyptian scorpion) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.53 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 | 6atw.cif.gz | 17.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6atw.ent.gz | 11.4 KB | Display | PDB format |
PDBx/mmJSON format | 6atw.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6atw_validation.pdf.gz | 370.3 KB | Display | wwPDB validaton report |
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Full document | 6atw_full_validation.pdf.gz | 370.3 KB | Display | |
Data in XML | 6atw_validation.xml.gz | 4 KB | Display | |
Data in CIF | 6atw_validation.cif.gz | 5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/at/6atw ftp://data.pdbj.org/pub/pdb/validation_reports/at/6atw | HTTPS FTP |
-Related structure data
Related structure data | 6atlC 6atnC 6atsC 6atuC 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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-Components
#1: Protein/peptide | Mass: 4155.942 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Leiurus quinquestriatus quinquestriatus (Egyptian scorpion) Cell (production host): HEK-293F / Production host: Homo sapiens (human) / References: UniProt: P45639 |
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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: 1.71 Å3/Da / Density % sol: 28.23 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7 Details: 1.1 M Na malonate pH 7.0, 0.1 M HEPES pH 7.0, 0.5 % Jeffamine ED-2001 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: Mar 9, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54 Å / Relative weight: 1 |
Reflection | Resolution: 1.53→50 Å / Num. obs: 7263 / % possible obs: 86.9 % / Redundancy: 13.1 % / Rmerge(I) obs: 0.095 / Rpim(I) all: 0.023 / Net I/σ(I): 13.1 |
Reflection shell | Resolution: 1.53→1.56 Å / Redundancy: 2.3 % / Rmerge(I) obs: 0.126 / Num. unique obs: 46 / CC1/2: 0.935 / Rpim(I) all: 0.076 / % possible all: 10.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.53→24.02 Å / Cor.coef. Fo:Fc: 0.974 / Cor.coef. Fo:Fc free: 0.948 / SU B: 1.065 / SU ML: 0.04 / Cross valid method: THROUGHOUT / ESU R: 0.081 / ESU R Free: 0.087 / 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: 15.516 Å2
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Refinement step | Cycle: 1 / Resolution: 1.53→24.02 Å
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Refine LS restraints |
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