[English] 日本語
Yorodumi- PDB-2bqy: Inorganic Pyrophosphatase from the Pathogenic Bacterium Helicobac... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2bqy | ||||||
---|---|---|---|---|---|---|---|
Title | Inorganic Pyrophosphatase from the Pathogenic Bacterium Helicobacter pylori-Kinetic and Structural Properties | ||||||
Components | INORGANIC PYROPHOSPHATASE | ||||||
Keywords | HYDROLASE / INORGANIC PYROPHOSPHATASE / HELICOBACTER PYLORI | ||||||
Function / homology | Function and homology information inorganic diphosphatase / inorganic diphosphate phosphatase activity / phosphate-containing compound metabolic process / magnesium ion binding / cytosol Similarity search - Function | ||||||
Biological species | HELICOBACTER PYLORI (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å | ||||||
Authors | Chao, T.-C. / Sun, Y.-J. | ||||||
Citation | Journal: Proteins / Year: 2006 Title: Kinetic and Structural Properties of Inorganic Pyrophosphatase from the Pathogenic Bacterium Helicobacter Pylori. Authors: Chao, T.-C. / Huang, H. / Tsai, J.Y. / Huang, C.Y. / Sun, Y.-J. | ||||||
History |
| ||||||
Remark 700 | SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AA" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 5-STRANDED BARREL THIS IS REPRESENTED BY A 6-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 2bqy.cif.gz | 46.9 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb2bqy.ent.gz | 33.6 KB | Display | PDB format |
PDBx/mmJSON format | 2bqy.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2bqy_validation.pdf.gz | 438.9 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 2bqy_full_validation.pdf.gz | 441.8 KB | Display | |
Data in XML | 2bqy_validation.xml.gz | 9.7 KB | Display | |
Data in CIF | 2bqy_validation.cif.gz | 12.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bq/2bqy ftp://data.pdbj.org/pub/pdb/validation_reports/bq/2bqy | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| x 6||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 19297.938 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) HELICOBACTER PYLORI (bacteria) / Strain: 26695 / Plasmid: PQE30 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): SG13009 / References: UniProt: P56153, inorganic diphosphatase |
---|---|
#2: Chemical | ChemComp-POP / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 3.44 Å3/Da / Density % sol: 64 % |
---|
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: NSRRC / Beamline: BL17B2 / Wavelength: 1.12714 |
Detector | Type: ADSC CCD / Detector: CCD / Date: Apr 15, 2004 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.12714 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→19.91 Å / Num. obs: 146975 / % possible obs: 99.3 % / Observed criterion σ(I): 2 / Redundancy: 11 % / Biso Wilson estimate: 38.1 Å2 / Rmerge(I) obs: 0.09 / Net I/σ(I): 24 |
Reflection shell | Resolution: 2.3→2.44 Å / Redundancy: 7 % / Rmerge(I) obs: 0.48 / Mean I/σ(I) obs: 4.7 / % possible all: 100 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.3→19.91 Å / Rfactor Rfree error: 0.011 / Data cutoff high absF: 541678.73 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Solvent model: FLAT MODEL / Bsol: 40.9642 Å2 / ksol: 0.382943 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 43.4 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.3→19.91 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.3→2.44 Å / Rfactor Rfree error: 0.043 / Total num. of bins used: 6
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Xplor file |
|