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Yorodumi- PDB-3vnc: Crystal Structure of TIP-alpha N25 from Helicobacter Pylori in it... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3vnc | ||||||
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Title | Crystal Structure of TIP-alpha N25 from Helicobacter Pylori in its natural dimeric form | ||||||
Components | TIP-alpha | ||||||
Keywords | DNA BINDING PROTEIN / TNF-alpha-inducing Protein / HP0596 / Homodimer / Carcinogenic Factor | ||||||
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 / Tumor necrosis factor alpha-inducing protein Function and homology information | ||||||
Biological species | Helicobacter pylori (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.6 Å | ||||||
Authors | Gao, M. / Li, D. / Hu, Y. / Zou, Q. / Wang, D.-C. | ||||||
Citation | Journal: Plos One / Year: 2012 Title: Crystal Structure of TNF-alpha-Inducing Protein from Helicobacter Pylori in Active Form Reveals the Intrinsic Molecular Flexibility for Unique DNA-Binding Authors: Gao, M. / Li, D. / Hu, Y. / Zhang, Y. / Zou, Q. / Wang, D.-C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3vnc.cif.gz | 71.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3vnc.ent.gz | 53.6 KB | Display | PDB format |
PDBx/mmJSON format | 3vnc.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3vnc_validation.pdf.gz | 433.4 KB | Display | wwPDB validaton report |
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Full document | 3vnc_full_validation.pdf.gz | 442.4 KB | Display | |
Data in XML | 3vnc_validation.xml.gz | 14.2 KB | Display | |
Data in CIF | 3vnc_validation.cif.gz | 18.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vn/3vnc ftp://data.pdbj.org/pub/pdb/validation_reports/vn/3vnc | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 19223.031 Da / Num. of mol.: 2 / Fragment: Residues 25-192 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Helicobacter pylori (bacteria) / Strain: 26695 / Gene: HP_0596 / Plasmid: pET22b / Production host: Escherichia coli (E. coli) / Strain (production host): BL(DE3) / References: UniProt: O25318 #2: 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: 3.32 Å3/Da / Density % sol: 62.9 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4 Details: 16% PEG3350, 80% Tacsimate, 2% 1,2-propanediol, 5% MPD, 5% Glycerol, pH 4, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 90 K | ||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: BL-17A / Wavelength: 0.97898, 0.97917, 0.96395 | ||||||||||||
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 26, 2009 | ||||||||||||
Radiation | Monochromator: Numerical link type Si(111) double crystal monochromator Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||
Radiation wavelength |
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Reflection | Resolution: 2.6→49.14 Å / Num. all: 15779 / Num. obs: 15054 / % possible obs: 95.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.2 % / Biso Wilson estimate: 37.1 Å2 / Rmerge(I) obs: 0.102 / Rsym value: 0.102 / Net I/σ(I): 17.7 | ||||||||||||
Reflection shell | Resolution: 2.6→2.74 Å / Redundancy: 7.3 % / Rmerge(I) obs: 0.374 / Mean I/σ(I) obs: 4.7 / Num. unique all: 2289 / Rsym value: 0.374 / % possible all: 99.9 |
-Processing
Software |
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Refinement | Method to determine structure: MAD / Resolution: 2.6→49.14 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 2045408.21 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber / Details: BULK SOLVENT MODEL USED
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 58.6298 Å2 / ksol: 0.4 e/Å3 | |||||||||||||||||||||||||
Displacement parameters | Biso mean: 48.7 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.6→49.14 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.6→2.76 Å / Rfactor Rfree error: 0.026 / Total num. of bins used: 6
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Xplor file |
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