[English] 日本語
Yorodumi- PDB-3gio: Crystal structure of the TNF-alpha inducing protein (Tip alpha) f... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3gio | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of the TNF-alpha inducing protein (Tip alpha) from Helicobacter pylori | ||||||
Components | Putative uncharacterized protein | ||||||
Keywords | DNA BINDING PROTEIN / antiparallel beta sheet / four-helix bundle / loop | ||||||
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: 2.4 Å | ||||||
Authors | Jang, J.Y. / Yoon, H.J. / Yoon, J.Y. / Kim, H.S. / Lee, S.J. / Kim, K.H. / Kim, D.J. / Han, B.G. / Lee, B.I. / Jang, S. / Suh, S.W. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2009 Title: Crystal Structure of the TNF-alpha-Inducing Protein (Tipalpha) from Helicobacter pylori: Insights into Its DNA-Binding Activity. Authors: Jang, J.Y. / Yoon, H.J. / Yoon, J.Y. / Kim, H.S. / Lee, S.J. / Kim, K.H. / Kim, D.J. / Jang, S. / Han, B.G. / Lee, B.I. / Suh, S.W. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 3gio.cif.gz | 69.1 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb3gio.ent.gz | 55.8 KB | Display | PDB format |
PDBx/mmJSON format | 3gio.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3gio_validation.pdf.gz | 440.3 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 3gio_full_validation.pdf.gz | 448.9 KB | Display | |
Data in XML | 3gio_validation.xml.gz | 14.4 KB | Display | |
Data in CIF | 3gio_validation.cif.gz | 18.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gi/3gio ftp://data.pdbj.org/pub/pdb/validation_reports/gi/3gio | HTTPS FTP |
-Related structure data
Similar structure data |
---|
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 21452.682 Da / Num. of mol.: 2 / Fragment: UNP residues 28-192 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Helicobacter pylori (bacteria) / Strain: 26695 / Gene: HP_0596 / Plasmid: pET-28b(+) / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta2(DE3)pLysS / References: UniProt: O25318 #2: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 2 |
---|
-Sample preparation
Crystal | Density Matthews: 1.91 Å3/Da / Density % sol: 35.6 % |
---|---|
Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 100mM Tris-HCl (pH 7.0), 200mM calcium acetate, 20% (w/v) PEG 3000, VAPOR DIFFUSION, HANGING DROP, temperature 295K |
-Data collection
Diffraction |
| |||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Diffraction source |
| |||||||||||||||
Detector |
| |||||||||||||||
Radiation |
| |||||||||||||||
Radiation wavelength |
| |||||||||||||||
Reflection | Resolution: 2.4→30 Å / Num. obs: 13650 / % possible obs: 100 % / Redundancy: 15.7 % / Rmerge(I) obs: 0.093 / Net I/σ(I): 42.9 | |||||||||||||||
Reflection shell | Resolution: 2.4→2.49 Å / Rmerge(I) obs: 0.422 / Mean I/σ(I) obs: 7.2 / Num. unique all: 1341 / % possible all: 100 |
-Processing
Software |
| |||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MAD / Resolution: 2.4→30 Å / σ(F): 0
| |||||||||||||||||||||||||
Displacement parameters |
| |||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.4→30 Å
|