+Open data
-Basic information
Entry | Database: PDB / ID: 6ay7 | ||||||
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Title | Cartilage homing cysteine-dense-peptides | ||||||
Components | Potassium channel toxin alpha-KTx 3.5 | ||||||
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 / trifluoroacetic acid / Potassium channel toxin alpha-KTx 3.5 Function and homology information | ||||||
Biological species | Androctonus australis (Sahara scorpion) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.77 Å | ||||||
Authors | Gewe, M.M. / Strong, R.K. | ||||||
Citation | Journal: To Be Published Title: Cartilage homing cysteine-dense-peptides Authors: Gewe, M.M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6ay7.cif.gz | 31.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6ay7.ent.gz | 19.9 KB | Display | PDB format |
PDBx/mmJSON format | 6ay7.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ay/6ay7 ftp://data.pdbj.org/pub/pdb/validation_reports/ay/6ay7 | HTTPS FTP |
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-Related structure data
Related structure data | 6ay8C 6atmS 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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2 |
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Unit cell |
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-Components
#1: Protein/peptide | Mass: 4349.137 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Androctonus australis (Sahara scorpion) Gene: KTX2 / Cell (production host): HEK-293F / Production host: Homo sapiens (human) / References: UniProt: P45696 #2: Chemical | #3: Chemical | #4: Chemical | #5: 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: 1.83 Å3/Da / Density % sol: 32.79 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 4.2 Details: 0.2M Na chloride, 0.1M Phosphate-citrate pH 4.2, 20% PEG 8000 |
-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 20, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54 Å / Relative weight: 1 |
Reflection | Resolution: 1.77→50 Å / Num. obs: 5643 / % possible obs: 80.9 % / Redundancy: 5.4 % / Rmerge(I) obs: 0.056 / Rpim(I) all: 0.025 / Net I/σ(I): 32.4 |
Reflection shell | Resolution: 1.77→1.8 Å / Redundancy: 1.6 % / Rmerge(I) obs: 0.11 / Mean I/σ(I) obs: 8.4 / Num. unique obs: 34 / CC1/2: 0.995 / Rpim(I) all: 0.106 / % possible all: 9.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6ATM Resolution: 1.77→33.81 Å / Cor.coef. Fo:Fc: 0.974 / Cor.coef. Fo:Fc free: 0.949 / SU B: 2.281 / SU ML: 0.072 / Cross valid method: THROUGHOUT / ESU R: 0.143 / ESU R Free: 0.134 / 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: 16.713 Å2
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Refinement step | Cycle: 1 / Resolution: 1.77→33.81 Å
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Refine LS restraints |
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