+Open data
-Basic information
Entry | Database: PDB / ID: 4om5 | ||||||
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Title | Crystal structure of CTX A4 from Taiwan Cobra (Naja naja atra) | ||||||
Components | Cytotoxin 4 | ||||||
Keywords | TOXIN / Five beta sheets / three functional loops / endocytosis / heparin / heparan sulfate | ||||||
Function / homology | Function and homology information other organism cell membrane / protein kinase inhibitor activity / toxin activity / killing of cells of another organism / extracellular region / membrane Similarity search - Function | ||||||
Biological species | Naja atra (Chinese cobra) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.55 Å | ||||||
Authors | Lin, C.C. / Chang, C.I. / Wu, W.G. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2014 Title: Endocytotic Routes of Cobra Cardiotoxins Depend on Spatial Distribution of Positively Charged and Hydrophobic Domains to Target Distinct Types of Sulfated Glycoconjugates on Cell Surface. Authors: Lee, S.C. / Lin, C.C. / Wang, C.H. / Wu, P.L. / Huang, H.W. / Chang, C.I. / Wu, W.G. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4om5.cif.gz | 102.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4om5.ent.gz | 87 KB | Display | PDB format |
PDBx/mmJSON format | 4om5.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4om5_validation.pdf.gz | 442.2 KB | Display | wwPDB validaton report |
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Full document | 4om5_full_validation.pdf.gz | 442.8 KB | Display | |
Data in XML | 4om5_validation.xml.gz | 10.8 KB | Display | |
Data in CIF | 4om5_validation.cif.gz | 14.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/om/4om5 ftp://data.pdbj.org/pub/pdb/validation_reports/om/4om5 | 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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Details | The biological assembly is an oligomer. |
-Components
#1: Protein | Mass: 6804.278 Da / Num. of mol.: 4 / Fragment: UNP residues 22-81 / Source method: isolated from a natural source / Source: (natural) Naja atra (Chinese cobra) / Secretion: venom / References: UniProt: P01443 #2: Water | ChemComp-HOH / | |
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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: 3.52 Å3/Da / Density % sol: 65.04 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: 1.3 M ammonium sulfate, 100 mM Tris-HCl, 200 mM lithium sulfate, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K |
-Data collection
Diffraction | Mean temperature: 200 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B2 / Wavelength: 1 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: RAYONIX MX-225 / Detector: CCD / Date: Jul 4, 2009 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: Fixed exit double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.55→50 Å / Num. all: 13697 / Num. obs: 13697 / % possible obs: 100 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 41.1 % / Rmerge(I) obs: 0.15 / Net I/σ(I): 6.8 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.55→31.05 Å / Cor.coef. Fo:Fc: 0.931 / Cor.coef. Fo:Fc free: 0.903 / SU B: 17.426 / SU ML: 0.174 / Cross valid method: THROUGHOUT / ESU R: 0.343 / ESU R Free: 0.264 / 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: 42.246 Å2
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Refinement step | Cycle: LAST / Resolution: 2.55→31.05 Å
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Refine LS restraints |
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