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Yorodumi- PDB-5do6: Crystal structure of Dendroaspis polylepis venom mambalgin-1 T23A... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5do6 | ||||||
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Title | Crystal structure of Dendroaspis polylepis venom mambalgin-1 T23A mutant | ||||||
Components | Mambalgin-1 | ||||||
Keywords | TOXIN / Acid Sensing Ion Channels / Pain suppression Drug / Elapid Venom polypeptide | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Dendroaspis polylepis polylepis (black mamba) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.697 Å | ||||||
Authors | Stura, E.A. / Tepshi, L. / Kessler, P. / Gilles, M. / Servent, D. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2016 Title: Mambalgin-1 Pain-relieving Peptide, Stepwise Solid-phase Synthesis, Crystal Structure, and Functional Domain for Acid-sensing Ion Channel 1a Inhibition. Authors: Mourier, G. / Salinas, M. / Kessler, P. / Stura, E.A. / Leblanc, M. / Tepshi, L. / Besson, T. / Diochot, S. / Baron, A. / Douguet, D. / Lingueglia, E. / Servent, D. #1: Journal: J Synchrotron Radiat / Year: 2017 Title: Comparison of helical scan and standard rotation methods in single-crystal X-ray data collection strategies. Authors: Polsinelli, I. / Savko, M. / Rouanet-Mehouas, C. / Ciccone, L. / Nencetti, S. / Orlandini, E. / Stura, E.A. / Shepard, W. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5do6.cif.gz | 38.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5do6.ent.gz | 29.6 KB | Display | PDB format |
PDBx/mmJSON format | 5do6.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5do6_validation.pdf.gz | 446.5 KB | Display | wwPDB validaton report |
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Full document | 5do6_full_validation.pdf.gz | 446.6 KB | Display | |
Data in XML | 5do6_validation.xml.gz | 9.4 KB | Display | |
Data in CIF | 5do6_validation.cif.gz | 12.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/do/5do6 ftp://data.pdbj.org/pub/pdb/validation_reports/do/5do6 | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 6544.618 Da / Num. of mol.: 2 / Fragment: UNP residues 22-78 / Mutation: T23A / Source method: obtained synthetically / Details: T23A mutant Source: (synth.) Dendroaspis polylepis polylepis (black mamba) References: UniProt: P0DKR6 #2: Chemical | ChemComp-IOD / #3: Chemical | ChemComp-EDO / | #4: Chemical | ChemComp-PGO / | #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.88 Å3/Da / Density % sol: 57.34 % / Description: Prismatic crystals |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.6 Details: Protein: redissolved from lyophilized at 5mg/ml mamb-1-T23A in 50mM Na Acetate, pH 5.5. Precipitant: 21.6% PEG600, 3.6% PEG 20K 0.18M mixed L-malic acid, MES, Tris (pH4) and mixed sodium ...Details: Protein: redissolved from lyophilized at 5mg/ml mamb-1-T23A in 50mM Na Acetate, pH 5.5. Precipitant: 21.6% PEG600, 3.6% PEG 20K 0.18M mixed L-malic acid, MES, Tris (pH4) and mixed sodium Malonate, imidazole, boric acid(pH10) in the ratio 40:60. Cryoprotectant: 30% MPEG 550, 40% CryoProtX cryomix9, 10% NaAc pH 6.5, 0.1M potassium iodide soaked for 1 min. PH range: 5.5 - 7.6 / Temp details: cooled incubator |
-Data collection
Diffraction | Mean temperature: 100 K / Ambient temp details: N2 cryostat - Helical scan |
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Diffraction source | Source: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 2 / Wavelength: 0.9801 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 3, 2015 / Details: X-ray centering - Helical scan |
Radiation | Monochromator: [111] Si Cut monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9801 Å / Relative weight: 1 |
Reflection | Resolution: 1.697→37 Å / Num. all: 16719 / Num. obs: 31543 / % possible obs: 97.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 7.1 % / Rmerge(I) obs: 0.061 / Rsym value: 0.057 / Net I/σ(I): 21.83 |
Reflection shell | Resolution: 1.697→1.74 Å / Redundancy: 4.8 % / Rmerge(I) obs: 0.408 / Mean I/σ(I) obs: 4.64 / % possible all: 78.7 |
-Processing
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Refinement | Method to determine structure: SAD / Resolution: 1.697→27.95 Å / SU ML: 0.16 / Cross valid method: THROUGHOUT / σ(F): 1.38 / Phase error: 21.25 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.697→27.95 Å
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Refine LS restraints |
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LS refinement shell |
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