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Yorodumi- PDB-7soh: Exploring Cystine Dense Peptide Space to Open a Unique Molecular ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7soh | ||||||
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Title | Exploring Cystine Dense Peptide Space to Open a Unique Molecular Toolbox | ||||||
Components | Chlorotoxin | ||||||
Keywords | TOXIN / CDP / Chlorotoxin | ||||||
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 / molecular replacement / Resolution: 1.81 Å | ||||||
Authors | Gewe, M.M. / Strong, R.K. | ||||||
Funding support | 1items
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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 | 7soh.cif.gz | 20.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7soh.ent.gz | 10.3 KB | Display | PDB format |
PDBx/mmJSON format | 7soh.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7soh_validation.pdf.gz | 393.8 KB | Display | wwPDB validaton report |
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Full document | 7soh_full_validation.pdf.gz | 393.8 KB | Display | |
Data in XML | 7soh_validation.xml.gz | 3.5 KB | Display | |
Data in CIF | 7soh_validation.cif.gz | 4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/so/7soh ftp://data.pdbj.org/pub/pdb/validation_reports/so/7soh | HTTPS FTP |
-Related structure data
Related structure data | 6atwS S: Starting model for refinement |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein/peptide | Mass: 4239.984 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Leiurus quinquestriatus quinquestriatus (Egyptian scorpion) 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: 1.67 Å3/Da / Density % sol: 26.29 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 8.5 / Details: 0.2 M tri-Potassium Citrate, 20% (w/v) PEG3350 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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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: Oct 7, 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: 1.81→50 Å / Num. obs: 2451 / % possible obs: 86 % / Redundancy: 5.4 % / CC1/2: 0.988 / Rmerge(I) obs: 0.057 / Rrim(I) all: 0.064 / Net I/σ(I): 33 |
Reflection shell | Resolution: 1.81→1.875 Å / Num. unique obs: 91 / CC1/2: 0.95 / % possible all: 15.6 |
-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6ATW Resolution: 1.81→23.87 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.916 / SU B: 3.172 / SU ML: 0.09 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.167 / ESU R Free: 0.144 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 34.08 Å2 / Biso mean: 13.514 Å2 / Biso min: 7.24 Å2
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Refinement step | Cycle: final / Resolution: 1.81→23.87 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.81→1.853 Å / Rfactor Rfree error: 0
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