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Yorodumi- PDB-2yj6: Conformational changes in the catalytic domain of the CPx-ATPase ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2yj6 | ||||||
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Title | Conformational changes in the catalytic domain of the CPx-ATPase CopB- B upon nucleotide binding | ||||||
Components | COPPER-TRANSPORTING ATPASE | ||||||
Keywords | HYDROLASE / P-TYPE ATPASE / HEAVY METAL TRANSLOCATION | ||||||
Function / homology | Function and homology information H+/K+-exchanging ATPase / ATPase-coupled monoatomic cation transmembrane transporter activity / transmembrane transporter activity / transmembrane transport / ATP hydrolysis activity / ATP binding / membrane / metal ion binding Similarity search - Function | ||||||
Biological species | SULFOLOBUS SOLFATARICUS (archaea) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å | ||||||
Authors | Voellmecke, C. / Schlicker, C. / Luebben, M. / Hofmann, E. | ||||||
Citation | Journal: To be Published Title: Conformational Changes in the Catalytic Domain of the Cpx-ATPase Copb-B Upon Nucleotide Binding Authors: Voellmecke, C. / Schlicker, C. / Luebben, M. / Hofmann, E. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2yj6.cif.gz | 108.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2yj6.ent.gz | 82.9 KB | Display | PDB format |
PDBx/mmJSON format | 2yj6.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yj/2yj6 ftp://data.pdbj.org/pub/pdb/validation_reports/yj/2yj6 | HTTPS FTP |
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-Related structure data
Related structure data | 2yj3C 2yj4C 2yj5C 2iyeS C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-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
#1: Protein | Mass: 28825.393 Da / Num. of mol.: 2 / Fragment: RESIDUES 383-645 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) SULFOLOBUS SOLFATARICUS (archaea) / Strain: P2 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) References: UniProt: Q97UU7, EC: 3.6.1.36, H+/K+-exchanging ATPase #2: Chemical | #3: Chemical | ChemComp-PO4 / | #4: Water | ChemComp-HOH / | Compound details | ENGINEERED | |
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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: 2.58 Å3/Da / Density % sol: 52.36 % / Description: NONE |
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Crystal grow | Details: 0.1 M NA/MES PH 6.5, 0.2 M AMMONIUM CHLORIDE, 15 % PEG 6000 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1 |
Detector | Type: DECTRIS PILATUS / Detector: PIXEL |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→48.33 Å / Num. obs: 29666 / % possible obs: 99.9 % / Observed criterion σ(I): 2 / Redundancy: 6.6 % / Biso Wilson estimate: 40.18 Å2 / Rmerge(I) obs: 0.05 / Net I/σ(I): 21.25 |
Reflection shell | Resolution: 2.2→2.3 Å / Redundancy: 7 % / Rmerge(I) obs: 0.35 / Mean I/σ(I) obs: 5.82 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2IYE Resolution: 2.2→48.33 Å / SU ML: 0.42 / σ(F): 1.99 / Phase error: 30.22 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 1.06 Å / VDW probe radii: 1.3 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 38.79 Å2 / ksol: 0.3 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 42.4 Å2
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Refinement step | Cycle: LAST / Resolution: 2.2→48.33 Å
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Refine LS restraints |
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LS refinement shell |
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