[English] 日本語
Yorodumi- PDB-1ihu: CRYSTAL STRUCTURE OF THE ESCHERICHIA COLI ARSENITE-TRANSLOCATING ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1ihu | ||||||
---|---|---|---|---|---|---|---|
Title | CRYSTAL STRUCTURE OF THE ESCHERICHIA COLI ARSENITE-TRANSLOCATING ATPASE IN COMPLEX WITH MG-ADP-ALF3 | ||||||
Components | ARSENICAL PUMP-DRIVING ATPASE | ||||||
Keywords | HYDROLASE / Aluminum Fluoride / ADP / ArsA ATPase / ATP binding site | ||||||
Function / homology | Function and homology information arsenite-transporting ATPase / ATPase-coupled arsenite transmembrane transporter activity / ATP hydrolysis activity / ATP binding Similarity search - Function | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.15 Å | ||||||
Authors | Zhou, T. / Radaev, S. / Rosen, B.P. / Gatti, D.L. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2001 Title: Conformational changes in four regions of the Escherichia coli ArsA ATPase link ATP hydrolysis to ion translocation. Authors: Zhou, T. / Radaev, S. / Rosen, B.P. / Gatti, D.L. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 1ihu.cif.gz | 126.9 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb1ihu.ent.gz | 96.4 KB | Display | PDB format |
PDBx/mmJSON format | 1ihu.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ih/1ihu ftp://data.pdbj.org/pub/pdb/validation_reports/ih/1ihu | HTTPS FTP |
---|
-Related structure data
-Links
-Assembly
Deposited unit |
| |||||||||
---|---|---|---|---|---|---|---|---|---|---|
1 |
| |||||||||
2 |
| |||||||||
Unit cell |
| |||||||||
Components on special symmetry positions |
|
-Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 64084.992 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Gene: ARSA / Production host: Escherichia coli (E. coli) / References: UniProt: P08690, EC: 3.6.3.16 |
---|
-Non-polymers , 7 types, 209 molecules
#2: Chemical | #3: Chemical | ChemComp-CD / #4: Chemical | #5: Chemical | #6: Chemical | ChemComp-AF3 / | #7: Chemical | ChemComp-TAS / | #8: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.44 Å3/Da / Density % sol: 49.5 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Crystal grow | Temperature: 303 K / Method: vapor diffusion, hanging drop / pH: 8 Details: PEG3000, ADP, AlCl3, NaF, MgCl2, NaAsO2, CdCl2, Bistrispropane, pH 8, VAPOR DIFFUSION, HANGING DROP, temperature 303K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 30 ℃ / pH: 8 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
|
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å |
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Apr 1, 2000 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.15→25.15 Å / Num. all: 213945 / Num. obs: 213945 / % possible obs: 94.1 % / Observed criterion σ(I): 2 / Redundancy: 6.2 % / Biso Wilson estimate: 26.8 Å2 / Rmerge(I) obs: 0.077 / Net I/σ(I): 17.5 |
Reflection shell | Resolution: 2.15→2.38 Å / Rmerge(I) obs: 0.733 / Num. unique all: 3209 / % possible all: 93.4 |
Reflection | *PLUS Num. obs: 34275 / Num. measured all: 213945 |
-Processing
Software |
| |||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.15→25.15 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 331602.19 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2 / σ(I): 2 / Stereochemistry target values: Engh & Huber
| |||||||||||||||||||||||||
Solvent computation | Solvent model: FLAT MODEL / Bsol: 53.59 Å2 / ksol: 0.346 e/Å3 | |||||||||||||||||||||||||
Displacement parameters | Biso mean: 42.8 Å2
| |||||||||||||||||||||||||
Refine analyze |
| |||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.15→25.15 Å
| |||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||
LS refinement shell | Resolution: 2.15→2.23 Å / Rfactor Rfree error: 0.018 / Total num. of bins used: 6
| |||||||||||||||||||||||||
Xplor file |
| |||||||||||||||||||||||||
Software | *PLUS Name: CNS / Version: 1 / Classification: refinement | |||||||||||||||||||||||||
Refinement | *PLUS σ(F): 2 / % reflection Rfree: 8.1 % | |||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||
Displacement parameters | *PLUS Biso mean: 42.8 Å2 | |||||||||||||||||||||||||
Refine LS restraints | *PLUS
| |||||||||||||||||||||||||
LS refinement shell | *PLUS Rfactor Rfree: 0.342 / % reflection Rfree: 8.1 % / Rfactor Rwork: 0.316 |