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Yorodumi- PDB-3cwy: Structure of CagD from H. pylori pathogenicity island crystallize... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3cwy | ||||||
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Title | Structure of CagD from H. pylori pathogenicity island crystallized in the presence of Cu(II) ions | ||||||
Components | protein CagD | ||||||
Keywords | UNKNOWN FUNCTION / CagD / cag-pathogenicity island / Type IV secretion system / T4SS | ||||||
Function / homology | Pathogenicity island component CagD / Pathogenicity island component CagD / Pathogenicity island component CagD superfamily / Pathogenicity island component CagD / Inhibitor of vertebrate lysozyme, Ivy / 3-Layer(aba) Sandwich / Alpha Beta / COPPER (II) ION / CagD Function and homology information | ||||||
Biological species | Helicobacter pylori (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.75 Å | ||||||
Authors | Cendron, L. / Zanotti, G. / Angelini, A. / Barison, N. / Couturier, M. / Stein, M. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2009 Title: The Helicobacter pylori CagD (HP0545, Cag24) protein is essential for CagA translocation and maximal induction of interleukin-8 secretion. Authors: Cendron, L. / Couturier, M. / Angelini, A. / Barison, N. / Stein, M. / Zanotti, G. #1: Journal: J.Mol.Biol. / Year: 2004 Title: Crystal structure of CagZ, a protein from the Helicobacter pylori pathogenicity island that encodes for a type IV secretion system Authors: Cendron, L. / Seydel, A. / Angelini, A. / Battistutta, R. / Zanotti, G. #2: Journal: Proteins: Struct.,Funct.,Genet. / Year: 2007 Title: The crystal structure of CagS from the Helicobacter pylori pathogenicity island Authors: Cendron, L. / Tasca, E. / Seraglio, T. / Seydel, A. / Angelini, A. / Battistutta, R. / Montecucco, C. / Zanotti, G. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3cwy.cif.gz | 41.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3cwy.ent.gz | 28.4 KB | Display | PDB format |
PDBx/mmJSON format | 3cwy.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/cw/3cwy ftp://data.pdbj.org/pub/pdb/validation_reports/cw/3cwy | HTTPS FTP |
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-Related structure data
Related structure data | 3cwxSC S: Starting model for refinement C: citing same article (ref.) |
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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
#1: Protein | Mass: 20777.463 Da / Num. of mol.: 1 / Fragment: CagD / Mutation: V79M, V140M Source method: isolated from a genetically manipulated source Source: (gene. exp.) Helicobacter pylori (bacteria) / Strain: CCUG 17874 / Gene: cagD / Plasmid: pET28b-cagD / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) / References: UniProt: P94837 |
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#2: Chemical | ChemComp-CU / |
#3: 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: 2.29 Å3/Da / Density % sol: 46.38 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion / pH: 7 Details: 0.2 M MgCl2, 0.1 M Hepes pH 7, 20% PEG 6000, CuCl2 0.02M , VAPOR DIFFUSION, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.97621 Å |
Detector | Type: MAR CCD 165 mm / Detector: CCD / Date: Aug 31, 2007 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97621 Å / Relative weight: 1 |
Reflection | Resolution: 2.75→78.09 Å / Num. all: 5757 / Num. obs: 5757 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 10.3 % / Biso Wilson estimate: 21.5 Å2 / Rmerge(I) obs: 0.079 / Net I/σ(I): 7.5 |
Reflection shell | Resolution: 2.75→2.85 Å / Redundancy: 10.7 % / Rmerge(I) obs: 0.459 / Mean I/σ(I) obs: 1.7 / Num. unique all: 796 / % possible all: 99 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3CWX Resolution: 2.75→56.34 Å / Rfactor Rfree error: 0.019 / Data cutoff high absF: 1913839.91 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0
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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: FLAT MODEL / Bsol: 102.977 Å2 / ksol: 0.708042 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 56.67 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.75→56.34 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.75→2.82 Å / Rfactor Rfree error: 0.046 / Total num. of bins used: 20
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Xplor file |
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