+Open data
-Basic information
Entry | Database: PDB / ID: 4om4 | ||||||
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Title | Crystal structure of CTX A2 from Taiwan Cobra (Naja naja atra) | ||||||
Components | Cytotoxin 2 | ||||||
Keywords | TOXIN / Five beta sheets / three functional loops / endocytosis / heparin / heparan sulfate | ||||||
Function / homology | Function and homology information other organism cell membrane / 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: 2.74 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 | 4om4.cif.gz | 69.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4om4.ent.gz | 53.5 KB | Display | PDB format |
PDBx/mmJSON format | 4om4.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4om4_validation.pdf.gz | 456.8 KB | Display | wwPDB validaton report |
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Full document | 4om4_full_validation.pdf.gz | 462.5 KB | Display | |
Data in XML | 4om4_validation.xml.gz | 13.7 KB | Display | |
Data in CIF | 4om4_validation.cif.gz | 18.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/om/4om4 ftp://data.pdbj.org/pub/pdb/validation_reports/om/4om4 | HTTPS FTP |
-Related structure data
Related structure data | 4om5C 2bhiS 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 on special symmetry positions |
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Details | The biological assembly is an oligomer. |
-Components
#1: Protein | Mass: 6760.242 Da / Num. of mol.: 5 / Fragment: UNP residues 22-81 / Source method: isolated from a natural source / Source: (natural) Naja atra (Chinese cobra) / Secretion: venom / References: UniProt: P01442 #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: 4.28 Å3/Da / Density % sol: 71.25 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.2 Details: 5.5 M ammonium nitrate, 0.1 M Bis-Tris, pH 7.2, VAPOR DIFFUSION, HANGING DROP, temperature 291K |
-Data collection
Diffraction | Mean temperature: 200 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: NSRRC / Beamline: BL13B1 / Wavelength: 1 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Aug 4, 2009 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: LN2-cooled, 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: 2.74→30 Å / Num. all: 15886 / Num. obs: 15865 / % possible obs: 99.9 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 15.5 % / Rmerge(I) obs: 0.103 / Net I/σ(I): 13.2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2BHI Resolution: 2.74→25.62 Å / Cor.coef. Fo:Fc: 0.94 / Cor.coef. Fo:Fc free: 0.894 / SU B: 10.183 / SU ML: 0.205 / Cross valid method: THROUGHOUT / ESU R: 0.369 / ESU R Free: 0.291 / 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: 44.846 Å2
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Refinement step | Cycle: LAST / Resolution: 2.74→25.62 Å
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Refine LS restraints |
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