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Yorodumi- PDB-1f48: CRYSTAL STRUCTURE OF THE ESCHERICHIA COLI ARSENITE-TRANSLOCATING ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1f48 | ||||||
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Title | CRYSTAL STRUCTURE OF THE ESCHERICHIA COLI ARSENITE-TRANSLOCATING ATPASE | ||||||
Components | ARSENITE-TRANSLOCATING ATPASE | ||||||
Keywords | HYDROLASE / p-loop / antimonite binding site / ATP binding site | ||||||
Function / homology | Function and homology information arsenite-transporting ATPase / ATPase-coupled arsenite transmembrane transporter activity / post-translational protein targeting to endoplasmic reticulum membrane / ATP hydrolysis activity / ATP binding Similarity search - Function | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / Resolution: 2.3 Å | ||||||
Authors | Zhou, T. / Radaev, S. / Rosen, B.P. / Gatti, D.L. | ||||||
Citation | Journal: EMBO J. / Year: 2000 Title: Structure of the ArsA ATPase: the catalytic subunit of a heavy metal resistance pump. Authors: Zhou, T. / Radaev, S. / Rosen, B.P. / Gatti, D.L. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1f48.cif.gz | 127.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1f48.ent.gz | 97.8 KB | Display | PDB format |
PDBx/mmJSON format | 1f48.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1f48_validation.pdf.gz | 1 MB | Display | wwPDB validaton report |
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Full document | 1f48_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 1f48_validation.xml.gz | 26.8 KB | Display | |
Data in CIF | 1f48_validation.cif.gz | 37.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/f4/1f48 ftp://data.pdbj.org/pub/pdb/validation_reports/f4/1f48 | 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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2 |
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Unit cell |
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Components on special symmetry positions |
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-Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 64084.992 Da / Num. of mol.: 1 / Fragment: WHOLE PROTEIN WITH C-TERMINAL 6XHISTIDINE TAG Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Plasmid: R773 / Production host: Escherichia coli (E. coli) References: UniProt: P08690, Hydrolases; Acting on acid anhydrides; In phosphorus-containing anhydrides |
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-Non-polymers , 7 types, 234 molecules
#2: Chemical | #3: Chemical | #4: Chemical | ChemComp-CD / #5: Chemical | #6: Chemical | ChemComp-SBO / | #7: Chemical | #8: 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: 2.42 Å3/Da / Density % sol: 49.11 % | ||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 303 K / Method: vapor diffusion, hanging drop / pH: 8 Details: PEG 3000, ADP, magnesium chloride, antimonite, cadmium acetate, Bistrispropane, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 303K | ||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Details: Zhou, T., (1999) Acta Crystallogr., D55, 921. | ||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 |
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Aug 30, 1999 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→30 Å / Num. all: 27783 / Num. obs: 27783 / % possible obs: 98.2 % / Observed criterion σ(I): 2 / Redundancy: 6.4 % / Biso Wilson estimate: 36.1 Å2 / Rmerge(I) obs: 0.086 / Net I/σ(I): 18.8 |
Reflection shell | Resolution: 2.3→2.38 Å / Rmerge(I) obs: 0.651 / Num. unique all: 2527 / % possible all: 91.4 |
Reflection | *PLUS Num. measured all: 178456 |
Reflection shell | *PLUS % possible obs: 91.4 % / Mean I/σ(I) obs: 2.5 |
-Processing
Software |
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Refinement | Resolution: 2.3→26.37 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 430606.11 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 51.86 Å2 / ksol: 0.314 e/Å3 | ||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 50.6 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.3→26.37 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.3→2.44 Å / Rfactor Rfree error: 0.018 / Total num. of bins used: 6
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Xplor file |
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Software | *PLUS Name: CNS / Version: 1 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS σ(F): 0 / % reflection Rfree: 9.9 % | ||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS Biso mean: 50.6 Å2 | ||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor Rfree: 0.355 / % reflection Rfree: 10.1 % / Rfactor Rwork: 0.302 |