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Yorodumi- PDB-2wcq: Crystal Structure of Tip-Alpha N34 (HP0596) from Helicobacter pyl... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2wcq | ||||||
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Title | Crystal Structure of Tip-Alpha N34 (HP0596) from Helicobacter pylori at pH4 | ||||||
Components | TNF-ALPHA INDUCER PROTEIN | ||||||
Keywords | IMMUNE SYSTEM / HP0596 / TIP-ALPHA / HELICOBACTER PYLORI | ||||||
Function / homology | Helicobacter TNF-alpha-Inducing protein / Helicobacter TNF-alpha-inducing protein / TNF-alpha-Inducing protein of Helicobacter / Thiol Ester Dehydrase; Chain A / Prokaryotic membrane lipoprotein lipid attachment site profile. / Roll / Alpha Beta / CITRIC ACID / Tumor necrosis factor alpha-inducing protein Function and homology information | ||||||
Biological species | HELICOBACTER PYLORI (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.9 Å | ||||||
Authors | Tosi, T. / Cioci, G. / Jouravleva, K. / Dian, C. / Terradot, L. | ||||||
Citation | Journal: FEBS Lett. / Year: 2009 Title: Structures of the Tumor Necrosis Factor Alpha Inducing Protein Tipalpha: A Novel Virulence Factor from Helicobacter Pylori. Authors: Tosi, T. / Cioci, G. / Jouravleva, K. / Dian, C. / Terradot, L. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2wcq.cif.gz | 72.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2wcq.ent.gz | 54.5 KB | Display | PDB format |
PDBx/mmJSON format | 2wcq.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wc/2wcq ftp://data.pdbj.org/pub/pdb/validation_reports/wc/2wcq | HTTPS FTP |
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-Related structure data
-Links
-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: 18230.916 Da / Num. of mol.: 2 / Fragment: FRAGMENT AFTER TRYPSIN DIGESTION, RESIDUES 34-192 Source method: isolated from a genetically manipulated source Source: (gene. exp.) HELICOBACTER PYLORI (bacteria) / Plasmid: PET151-D TOPO / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / References: UniProt: O25318 #2: Chemical | #3: Water | ChemComp-HOH / | |
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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: 2.2 Å3/Da / Density % sol: 44 % / Description: NONE |
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Crystal grow | pH: 4 / Details: 100 MM CITRATE PH 4, 18% PEG 4000, 15 MM ATP |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.9395 |
Detector | Type: ADSC CCD / Detector: CCD / Details: MIRRORS |
Radiation | Monochromator: DIAMOND / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9395 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→50.96 Å / Num. obs: 22965 / % possible obs: 98.4 % / Observed criterion σ(I): 2 / Redundancy: 4.08 % / Biso Wilson estimate: 25.2 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 7.62 |
Reflection shell | Resolution: 1.9→2 Å / Redundancy: 3.56 % / Rmerge(I) obs: 0.33 / Mean I/σ(I) obs: 2.23 / % possible all: 90.4 |
-Processing
Software |
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Refinement | Method to determine structure: SAD Starting model: NONE Resolution: 1.9→47.14 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.933 / SU B: 3.51 / SU ML: 0.103 / Cross valid method: THROUGHOUT / ESU R: 0.171 / ESU R Free: 0.151 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY
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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: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 21.86 Å2
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Refinement step | Cycle: LAST / Resolution: 1.9→47.14 Å
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Refine LS restraints |
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