+Open data
-Basic information
Entry | Database: PDB / ID: 4tlv | ||||||
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Title | CARDS TOXIN, NICKED | ||||||
Components | ADP-ribosylating toxin CARDS | ||||||
Keywords | TOXIN / TRANSFERASE / MYCOPLASMA PNEUMONIAE / VIRULENCE / ATYPICAL PNEUMONIA / COMMUNITY ACQUIRED RESPIRATORY DISTRESS SYNDROME / ADP-RIBOSYL TRANSFERASE | ||||||
Function / homology | Function and homology information symbiont-mediated perturbation of host vacuole organization / attachment organelle / host cell cytosol / host cell endoplasmic reticulum / NAD+-protein poly-ADP-ribosyltransferase activity / Transferases; Glycosyltransferases; Pentosyltransferases / nucleotidyltransferase activity / cell projection / toxin activity / lipid binding ...symbiont-mediated perturbation of host vacuole organization / attachment organelle / host cell cytosol / host cell endoplasmic reticulum / NAD+-protein poly-ADP-ribosyltransferase activity / Transferases; Glycosyltransferases; Pentosyltransferases / nucleotidyltransferase activity / cell projection / toxin activity / lipid binding / cell surface / extracellular region / plasma membrane / cytoplasm Similarity search - Function | ||||||
Biological species | Mycoplasma pneumoniae (Filterable agent of primary atypical pneumonia) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SIRAS / Resolution: 1.9 Å | ||||||
Authors | Taylor, A.B. / Pakhomova, O.N. / Hart, P.J. | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2015 Title: Structure of CARDS toxin, a unique ADP-ribosylating and vacuolating cytotoxin from Mycoplasma pneumoniae. Authors: Becker, A. / Kannan, T.R. / Taylor, A.B. / Pakhomova, O.N. / Zhang, Y. / Somarajan, S.R. / Galaleldeen, A. / Holloway, S.P. / Baseman, J.B. / Hart, P.J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4tlv.cif.gz | 739.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4tlv.ent.gz | 608.5 KB | Display | PDB format |
PDBx/mmJSON format | 4tlv.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4tlv_validation.pdf.gz | 524.6 KB | Display | wwPDB validaton report |
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Full document | 4tlv_full_validation.pdf.gz | 560.4 KB | Display | |
Data in XML | 4tlv_validation.xml.gz | 135 KB | Display | |
Data in CIF | 4tlv_validation.cif.gz | 191.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/tl/4tlv ftp://data.pdbj.org/pub/pdb/validation_reports/tl/4tlv | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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Unit cell |
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-Components
#1: Protein | Mass: 68065.906 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mycoplasma pneumoniae (Filterable agent of primary atypical pneumonia) Strain: ATCC 29342 / M129 / Gene: MPN_372, MP464 / Plasmid: PKA8H / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) References: UniProt: P75409, Transferases; Glycosyltransferases; Pentosyltransferases #2: Chemical | ChemComp-SO4 / #3: Chemical | ChemComp-GOL / #4: Chemical | ChemComp-ACT / #5: Water | ChemComp-HOH / | Compound details | The CARDS toxin was treated with trypsin protease prior to crystallization, leaving a nicked ...The CARDS toxin was treated with trypsin protease prior to crystallization, leaving a nicked polypeptide with non-covalently associated domains defined by residues 1-305 and 308-591. The related un-nicked CARDS toxin in PDB entry 4TLW superimposes on each monomer of this entry with a RMSD of less than 0.4 Angstroms using alpha carbon positions. | |
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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: 2.8 Å3/Da / Density % sol: 56.09 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 4.6 Details: 1.6 M AMMONIUM SULFATE, 0.08 M SODIUM ACETATE, 20% GLYCEROL PH range: 4.6 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9795 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 13, 2009 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→50 Å / Num. obs: 350417 / % possible obs: 99.7 % / Redundancy: 3.1 % / Biso Wilson estimate: 22 Å2 / Rsym value: 0.073 / Net I/σ(I): 15.5 |
Reflection shell | Resolution: 1.9→1.97 Å / Redundancy: 3.2 % / Mean I/σ(I) obs: 2.3 / Rsym value: 0.577 / % possible all: 100 |
-Processing
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Refinement | Method to determine structure: SIRAS / Resolution: 1.9→38.87 Å / SU ML: 0.2 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 21.89 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.86 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 40 Å2 / ksol: 0.35 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 27.1 Å2
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Refinement step | Cycle: LAST / Resolution: 1.9→38.87 Å
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Refine LS restraints |
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LS refinement shell |
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