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- PDB-2yj6: Conformational changes in the catalytic domain of the CPx-ATPase ... -
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Open data
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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 | ||||||
![]() | COPPER-TRANSPORTING ATPASE | ||||||
![]() | HYDROLASE / P-TYPE ATPASE / HEAVY METAL TRANSLOCATION | ||||||
Function / homology | ![]() 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 | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Voellmecke, C. / Schlicker, C. / Luebben, M. / Hofmann, E. | ||||||
![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 108.8 KB | Display | ![]() |
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PDB format | ![]() | 82.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.1 MB | Display | ![]() |
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Full document | ![]() | 1.2 MB | Display | |
Data in XML | ![]() | 21.5 KB | Display | |
Data in CIF | ![]() | 28.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2yj3C ![]() 2yj4C ![]() 2yj5C ![]() 2iyeS C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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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.) ![]() ![]() ![]() ![]() 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: ![]() |
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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: ![]() ![]() ![]() |
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 |
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Processing
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Refinement | Method to determine structure: ![]() 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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