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- PDB-5dz5: Crystal structure of Dendroaspis polylepis mambalgin-1 wild-type ... -
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Open data
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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 | ||||||
![]() | Mambalgin-1 | ||||||
![]() | 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![]() | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Stura, E.A. / Tepshi, L. / Mourier, G. / Kessler, P. / Servent, D. | ||||||
![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 61.3 KB | Display | ![]() |
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PDB format | ![]() | 45 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 416.9 KB | Display | ![]() |
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Full document | ![]() | 417.6 KB | Display | |
Data in XML | ![]() | 7.3 KB | Display | |
Data in CIF | ![]() | 9.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5do6SC ![]() 5du1C C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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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.) ![]() References: UniProt: P0DKR6 #2: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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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: ![]() ![]() ![]() |
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 |
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Processing
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Refinement | Method to determine structure: ![]() 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 |