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Yorodumi- PDB-2g3v: Crystal structure of CagS (HP0534, Cag13) from Helicobacter pylori -
+Open data
-Basic information
Entry | Database: PDB / ID: 2g3v | ||||||
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Title | Crystal structure of CagS (HP0534, Cag13) from Helicobacter pylori | ||||||
Components |
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Keywords | UNKNOWN FUNCTION / Helicobacter pylori / pathogenicity island / Type IV secretion system | ||||||
Function / homology | CAG pathogenicity island protein 13, CagS / CAG pathogenicity island protein 13 / CagS superfamily / Cag pathogenicity island protein S of Helicobacter pylori / Four Helix Bundle (Hemerythrin (Met), subunit A) / Up-down Bundle / Mainly Alpha / CAG pathogenicity island protein 13 Function and homology information | ||||||
Biological species | Helicobacter pylori (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.3 Å | ||||||
Authors | Cendron, L. / Tasca, E. / Angelini, A. / Seydel, A. / Battistutta, R. / Montecucco, C. / Zanotti, G. | ||||||
Citation | Journal: To be Published Title: Crystal structure of CagS from helicobacter pylori Authors: Cendron, L. / Tasca, E. / Angelini, A. / Seydel, A. / Battistutta, R. / Montecucco, C. / 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. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2g3v.cif.gz | 147.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2g3v.ent.gz | 125.5 KB | Display | PDB format |
PDBx/mmJSON format | 2g3v.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2g3v_validation.pdf.gz | 473.4 KB | Display | wwPDB validaton report |
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Full document | 2g3v_full_validation.pdf.gz | 514.4 KB | Display | |
Data in XML | 2g3v_validation.xml.gz | 32.1 KB | Display | |
Data in CIF | 2g3v_validation.cif.gz | 44.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/g3/2g3v ftp://data.pdbj.org/pub/pdb/validation_reports/g3/2g3v | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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2 |
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3 |
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4 |
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Unit cell |
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-Components
#1: Protein | Mass: 25536.822 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Helicobacter pylori (bacteria) / Strain: G27 / Gene: cagS, cag13, HP0534 / Plasmid: pET21b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: P97227 #2: Protein/peptide | ( Mass: 706.735 Da / Num. of mol.: 4 / Source method: obtained synthetically / Details: The peptide was chemically synthesized. #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 3 |
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-Sample preparation
Crystal | Density Matthews: 2.2 Å3/Da / Density % sol: 43.2 % |
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Crystal grow | Temperature: 283 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: 0.2M KBr, 25% PEG 2000 MME, 0.1M Tris pH 8.5 , VAPOR DIFFUSION, HANGING DROP, temperature 283K |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.9792, 0.9794, 0.9756, 1.0 | |||||||||||||||
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Mar 12, 2005 / Details: Mirrors | |||||||||||||||
Radiation | Monochromator: Si(311) / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||
Radiation wavelength |
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Reflection | Resolution: 2.3→51 Å / Num. all: 38297 / Num. obs: 38297 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.8 % / Biso Wilson estimate: 6.7 Å2 / Rsym value: 0.011 / Net I/σ(I): 5 | |||||||||||||||
Reflection shell | Resolution: 2.3→2.42 Å / Redundancy: 4.9 % / Mean I/σ(I) obs: 1.7 / Num. unique all: 5569 / Rsym value: 0.41 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MAD / Resolution: 2.3→39.41 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 2250186.93 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 56.1075 Å2 / ksol: 0.40001 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 10.4 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.3→39.41 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.3→2.4 Å / Rfactor Rfree error: 0.015 / Total num. of bins used: 6
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Xplor file |
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