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Yorodumi- PDB-5dz5: Crystal structure of Dendroaspis polylepis mambalgin-1 wild-type ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5dz5 | ||||||
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Title | Crystal structure of Dendroaspis polylepis mambalgin-1 wild-type in P41212 space group | ||||||
Components | Mambalgin-1 | ||||||
Keywords | TOXIN / pain-relieving polypeptide / analgesic / Acid-Sensing Ion Channel / Mambalgin-1 / three-finger-fold | ||||||
Function / homology | ion channel regulator activity / CD59 / CD59 / Snake toxin-like superfamily / Ribbon / toxin activity / extracellular region / Mainly Beta / Mambalgin-1 Function and homology information | ||||||
Biological species | Dendroaspis polylepis polylepis (black mamba) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å | ||||||
Authors | Stura, E.A. / Tepshi, L. / Mourier, G. / Kessler, P. / 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. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5dz5.cif.gz | 61.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5dz5.ent.gz | 45 KB | Display | PDB format |
PDBx/mmJSON format | 5dz5.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5dz5_validation.pdf.gz | 283.5 KB | Display | wwPDB validaton report |
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Full document | 5dz5_full_validation.pdf.gz | 284.1 KB | Display | |
Data in XML | 5dz5_validation.xml.gz | 7.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dz/5dz5 ftp://data.pdbj.org/pub/pdb/validation_reports/dz/5dz5 | HTTPS FTP |
-Related structure data
Related structure data | 5do6SC 5du1C C: citing same article (ref.) S: Starting model for refinement |
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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 | Mass: 6574.644 Da / Num. of mol.: 2 / Source method: obtained synthetically Source: (synth.) Dendroaspis polylepis polylepis (black mamba) References: UniProt: P0DKR6 #2: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 1.68 Å3/Da / Density % sol: 26.7 % / Description: Prismatic |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7 Details: Protein: 5 mg/mL in 0.050 M Na Acetate, pH 5.5 Precipitant: 30% PEG600, 0.2 M Imidazole Malate, pH 7.0. Cryoprotectant: 40% CryoSol SM5, 30% PEG 600, 0.1 M mixed (Na acetate, ADA, Bicine) pH 7.0 PH range: 5.5-7.0 / Temp details: cooled incubator |
-Data collection
Diffraction | Mean temperature: 100 K / Ambient temp details: cryo-nozzle |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-1 / Wavelength: 0.965 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jan 29, 2015 / Details: automatic data collection on ESRF Massif1 ID30A-1 |
Radiation | Monochromator: diamond beam splitter / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.965 Å / Relative weight: 1 |
Reflection | Resolution: 1.95→46.8 Å / Num. all: 6985 / Num. obs: 6981 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 7.5 % / Rmerge(I) obs: 0.183 / Rsym value: 0.171 / Net I/σ(I): 9.66 |
Reflection shell | Resolution: 1.95→2 Å / Redundancy: 7.94 % / Rmerge(I) obs: 1.67 / Mean I/σ(I) obs: 1.19 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5DO6 Resolution: 1.95→40.467 Å / SU ML: 0.28 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 27.45 / 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: 1.95→40.467 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Origin x: -0.4511 Å / Origin y: 2.721 Å / Origin z: 7.7542 Å
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Refinement TLS group | Selection details: all |