+Open data
-Basic information
Entry | Database: PDB / ID: 4tlw | ||||||
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Title | CARDS TOXIN, FULL-LENGTH | ||||||
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+ 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+ 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 / MOLECULAR REPLACEMENT / Resolution: 2.55 Å | ||||||
Authors | Becker, A. / GALALELDEEN, A. / Taylor, A.B. / 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 | 4tlw.cif.gz | 129.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4tlw.ent.gz | 98.6 KB | Display | PDB format |
PDBx/mmJSON format | 4tlw.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/tl/4tlw ftp://data.pdbj.org/pub/pdb/validation_reports/tl/4tlw | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 70627.672 Da / Num. of mol.: 1 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 |
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#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.88 Å3/Da / Density % sol: 68.32 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.5 / Details: 30% PEG 1000, 0.1 M TRIS-HCL / PH range: 8.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.97903 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 8, 2010 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97903 Å / Relative weight: 1 |
Reflection | Resolution: 2.55→50 Å / Num. obs: 34160 / % possible obs: 99.1 % / Redundancy: 4.5 % / Biso Wilson estimate: 64.7 Å2 / Rsym value: 0.059 / Net I/σ(I): 20.5 |
Reflection shell | Resolution: 2.55→2.64 Å / Redundancy: 4.1 % / Mean I/σ(I) obs: 2.1 / Rsym value: 0.522 / % possible all: 93.2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.55→44.61 Å / SU ML: 0.41 / Cross valid method: THROUGHOUT / σ(F): 1.96 / Phase error: 31.78 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.7 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 61.47 Å2 / ksol: 0.34 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 77.8 Å2
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Refinement step | Cycle: LAST / Resolution: 2.55→44.61 Å
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Refine LS restraints |
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LS refinement shell |
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