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Yorodumi- PDB-4lft: Structure of alpha-elapitoxin-Dpp2d isolated from Black Mamba (De... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4lft | ||||||
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Title | Structure of alpha-elapitoxin-Dpp2d isolated from Black Mamba (Dendroaspis polylepis) venom | ||||||
Components | Alpha-elapitoxin-Dpp2a | ||||||
Keywords | TOXIN / Long neurotoxin / three-finger-toxin / disulfide-rich / acetylcholine receptor inhibitor activity / expressed by the venom gland | ||||||
Function / homology | Function and homology information host cell postsynaptic membrane / : / toxin activity / extracellular region Similarity search - Function | ||||||
Biological species | Dendroaspis polylepis polylepis (black mamba) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.7 Å | ||||||
Authors | Wang, C.I.A. / Reeks, T. / Lewis, R.J. / Alewood, P.F. / Durek, T. | ||||||
Citation | Journal: Biochemistry / Year: 2014 Title: Isolation and Structural and Pharmacological Characterization of alpha-Elapitoxin-Dpp2d, an Amidated Three Finger Toxin from Black Mamba Venom. Authors: Wang, C.I. / Reeks, T. / Vetter, I. / Vergara, I. / Kovtun, O. / Lewis, R.J. / Alewood, P.F. / Durek, T. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4lft.cif.gz | 41.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4lft.ent.gz | 28.9 KB | Display | PDB format |
PDBx/mmJSON format | 4lft.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4lft_validation.pdf.gz | 426.1 KB | Display | wwPDB validaton report |
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Full document | 4lft_full_validation.pdf.gz | 426.4 KB | Display | |
Data in XML | 4lft_validation.xml.gz | 8.9 KB | Display | |
Data in CIF | 4lft_validation.cif.gz | 12.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/lf/4lft ftp://data.pdbj.org/pub/pdb/validation_reports/lf/4lft | HTTPS FTP |
-Related structure data
Related structure data | 1ntnS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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Unit cell |
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-Components
#1: Protein | Mass: 8013.313 Da / Num. of mol.: 2 / Fragment: unp residues 65-136 / Source method: isolated from a natural source Details: Isolated from crude venom using cation-exchange chromatography and reversed-phase chromatography. Source: (natural) Dendroaspis polylepis polylepis (black mamba) References: UniProt: P01396 #2: Water | ChemComp-HOH / | Sequence details | AUTHORS HAVE DEPOSITED A NEW ALPHA ELAPITOCIN DPP2D SEQUENCE IN UNIPROT WITH THE ASSIGNED ACCESSION ...AUTHORS HAVE DEPOSITED A NEW ALPHA ELAPITOCIN | |
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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: 2.46 Å3/Da / Density % sol: 50.03 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: protein was dissolved in 2mM HCl, 5 mg/mL. reservoir: 0.1M TRIS-HCL, 2% (v/v) dioxane, 65% (v/v) 2-methyl-2,4-pentanediol (MPD), pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU FR-E SUPERBRIGHT / Wavelength: 1.54 Å |
Detector | Type: RIGAKU SATURN 944 / Detector: CCD / Date: Aug 24, 2012 |
Radiation | Monochromator: Mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→27.46 Å / Num. all: 121995 / Num. obs: 22047 / % possible obs: 92.85 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.53 % / Biso Wilson estimate: 23.903 Å2 / Rmerge(I) obs: 0.045 / Net I/σ(I): 27.2 |
Reflection shell | Resolution: 1.7→1.744 Å / Redundancy: 2.16 % / Rmerge(I) obs: 0.483 / Mean I/σ(I) obs: 1.9 / % possible all: 74.79 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1NTN Resolution: 1.7→27.46 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.94 / SU B: 1.917 / SU ML: 0.064 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.113 / ESU R Free: 0.107 / 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: 23.903 Å2
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Refinement step | Cycle: LAST / Resolution: 1.7→27.46 Å
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