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Yorodumi- PDB-5du1: Crystal structure of Dendroaspis polylepis mambalgin-1 wild-type ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5du1 | ||||||
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Title | Crystal structure of Dendroaspis polylepis mambalgin-1 wild-type in P21 space group. | ||||||
Components | Mambalgin-1 | ||||||
Keywords | TOXIN / Acid Sensing Ion Channels / Elapid Venoms / analgesic polypeptide | ||||||
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: 1.8 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 | 5du1.cif.gz | 63.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5du1.ent.gz | 46.9 KB | Display | PDB format |
PDBx/mmJSON format | 5du1.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5du1_validation.pdf.gz | 436 KB | Display | wwPDB validaton report |
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Full document | 5du1_full_validation.pdf.gz | 437 KB | Display | |
Data in XML | 5du1_validation.xml.gz | 12.6 KB | Display | |
Data in CIF | 5du1_validation.cif.gz | 18.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/du/5du1 ftp://data.pdbj.org/pub/pdb/validation_reports/du/5du1 | HTTPS FTP |
-Related structure data
Related structure data | 5do6SC 5dz5C 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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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: _ / Beg auth comp-ID: LEU / Beg label comp-ID: LEU / End auth comp-ID: LYS / End label comp-ID: LYS / Refine code: _ / Auth seq-ID: 1 - 57 / Label seq-ID: 1 - 57
NCS ensembles :
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-Components
#1: Protein | Mass: 6574.644 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Details: wild-type polypeptide found in the venom Source: (natural) 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: 1.74 Å3/Da / Density % sol: 29.41 % / Description: prismatic |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6 Details: protein: 5 mg/mL in 0.550 M Na Acetate pH 5.5 precipitant: 18% PEG4K, 3% MPD, 3% 1,4-dioxane, .188 M Imidazole Malate, pH 6 cryoprotectant:: CrySol-SM5, 30% PEG 600, 0.1 M mixed (Na acetate, ADA, Bicine), pH 7.5 PH range: 6-7.5 / Temp details: cooled incubator |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-1 / Wavelength: 0.965 Å |
Detector | Type: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Jan 29, 2015 Details: Compound Refractive Lens Fully automatic data collection |
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: 1.8→46.796 Å / Num. all: 15969 / Num. obs: 15969 / % possible obs: 93.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 2.7 % / Rmerge(I) obs: 0.063 / Rsym value: 0.052 / Net I/σ(I): 13.77 |
Reflection shell | Resolution: 1.8→1.91 Å / Redundancy: 2.77 % / Rmerge(I) obs: 0.257 / Mean I/σ(I) obs: 4.35 / % possible all: 84.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5DO6 Resolution: 1.8→38.96 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.936 / SU B: 3.832 / SU ML: 0.115 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.174 / ESU R Free: 0.153 / Stereochemistry target values: MAXIMUM LIKELIHOOD / 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 / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 27.705 Å2
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Refinement step | Cycle: 1 / Resolution: 1.8→38.96 Å
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Refine LS restraints |
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