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Open data
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Basic information
Entry | Database: PDB / ID: 8igu | |||||||||||||||
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Title | Hexameric Ring Complex of Engineered V1-ATPase: A3(De)3_empty | |||||||||||||||
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![]() | MOTOR PROTEIN / Computational Design / Rotary Molecular Motor / Complex | |||||||||||||||
Function / homology | ![]() Na+-transporting two-sector ATPase / sodium-transporting ATP synthase activity, rotational mechanism / sodium-transporting ATPase activity, rotational mechanism / sodium ion transport / proton motive force-driven plasma membrane ATP synthesis / proton-transporting ATP synthase complex / proton-transporting ATPase activity, rotational mechanism / proton-transporting ATP synthase activity, rotational mechanism / ATP binding Similarity search - Function | |||||||||||||||
Biological species | ![]() | |||||||||||||||
Method | ![]() ![]() ![]() | |||||||||||||||
![]() | Kosugi, T. / Tanabe, M. / Koga, N. | |||||||||||||||
Funding support | ![]()
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![]() | ![]() Title: Design of allosteric sites into rotary motor V 1 -ATPase by restoring lost function of pseudo-active sites. Authors: Kosugi, T. / Iida, T. / Tanabe, M. / Iino, R. / Koga, N. | |||||||||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 646.7 KB | Display | ![]() |
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PDB format | ![]() | Display | ![]() | |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 502.6 KB | Display | ![]() |
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Full document | ![]() | 573.1 KB | Display | |
Data in XML | ![]() | 123.7 KB | Display | |
Data in CIF | ![]() | 159.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8igvC ![]() 8igwC C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 66059.547 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Strain: ATCC 9790 / Gene: ntpA, EHR_08260 / Production host: ![]() ![]() References: UniProt: Q08636, Na+-transporting two-sector ATPase #2: Protein | Mass: 51017.219 Da / Num. of mol.: 3 Mutation: S151G, G152P, S153P, L155A, P156G, G157K, K158S, E159A, T248E, Q339S Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Strain: ATCC 9790 / Gene: ntpB, EHR_08265 / Production host: ![]() ![]() #3: Water | ChemComp-HOH / | Has protein modification | N | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.75 Å3/Da / Density % sol: 55.3 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop Details: 0.1 M Tris-HCl (pH 8.5), 24% PEG 3350 and 0.2 M Ammonium Acetate |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS EIGER X 4M / Detector: PIXEL / Date: Apr 22, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.1 Å / Relative weight: 1 |
Reflection | Resolution: 2.77→44.64 Å / Num. obs: 96837 / % possible obs: 100 % / Redundancy: 7 % / Biso Wilson estimate: 64.51 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.098 / Rpim(I) all: 0.04 / Net I/σ(I): 14.2 |
Reflection shell | Resolution: 2.77→2.82 Å / Redundancy: 7.3 % / Rmerge(I) obs: 0.876 / Mean I/σ(I) obs: 2.1 / Num. unique obs: 4764 / CC1/2: 0.728 / Rpim(I) all: 0.38 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]() Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.77→44.64 Å
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Refine LS restraints |
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LS refinement shell |
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