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- PDB-3cwx: Crystal structure of cagd from helicobacter pylori pathogenicity ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3cwx | ||||||
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Title | Crystal structure of cagd from helicobacter pylori pathogenicity island | ||||||
![]() | protein CagD | ||||||
![]() | 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 / CagD![]() | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Cendron, L. / Zanotti, G. / Angelini, A. / Barison, N. / Couturier, M. / Stein, M. | ||||||
![]() | ![]() 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: ![]() 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: ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 90.2 KB | Display | ![]() |
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PDB format | ![]() | 73.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 448.3 KB | Display | ![]() |
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Full document | ![]() | 471.2 KB | Display | |
Data in XML | ![]() | 19.8 KB | Display | |
Data in CIF | ![]() | 26.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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2 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 20777.463 Da / Num. of mol.: 3 / Fragment: CagD / Mutation: V79M, V140M Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #2: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.26 Å3/Da / Density % sol: 45.6 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion / pH: 7 Details: 0.2 M MgGl2, 0.1M Hepes, 20% PEG 6000, pH 7, VAPOR DIFFUSION, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | ||||||||||||
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 7, 2006 | ||||||||||||
Radiation | Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||
Radiation wavelength |
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Reflection | Resolution: 2.2→62.26 Å / Num. all: 28577 / Num. obs: 28577 / % possible obs: 99.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.3 % / Rmerge(I) obs: 0.088 / Net I/σ(I): 16.6 | ||||||||||||
Reflection shell | Resolution: 2.2→2.32 Å / Redundancy: 7.4 % / Rmerge(I) obs: 0.411 / Mean I/σ(I) obs: 4.1 / Num. unique all: 4107 / % possible all: 99.9 |
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Processing
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Refinement | Method to determine structure: ![]() Details: ANISOTROPIC SCALING APPLIED BY THE METHOD OF PARKIN, MOEZZI & HOPE, J.APPL.CRYST.28(1995)53-56
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Solvent computation | Solvent model: MOEWS & KRETSINGER, J.MOL.BIOL.91(1973)201-228 | |||||||||||||||||||||||||||||||||
Refine analyze | Num. disordered residues: 0 / Occupancy sum hydrogen: 0 / Occupancy sum non hydrogen: 3361 | |||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.3→62.26 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.3→2.4 Å
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