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- PDB-8igw: Hexameric Ring Complex of Engineered V1-ATPase bound to 4 ADPs: A... -
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Open data
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Basic information
Entry | Database: PDB / ID: 8igw | |||||||||||||||
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Title | Hexameric Ring Complex of Engineered V1-ATPase bound to 4 ADPs: A3(De)3_(ADP)3cat,1non-cat, Hexameric Ring Complex of Engineered V1-ATPase bound to 5 ADPs: A3(De)3_(ADP)3cat,2non-cat | |||||||||||||||
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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 / proton-transporting ATP synthase complex / vacuolar acidification / proton motive force-driven plasma membrane ATP synthesis / sodium ion transport / phagocytic vesicle / proton-transporting ATPase activity, rotational mechanism / proton-transporting ATP synthase activity, rotational mechanism ...Na+-transporting two-sector ATPase / sodium-transporting ATP synthase activity, rotational mechanism / sodium-transporting ATPase activity, rotational mechanism / proton-transporting ATP synthase complex / vacuolar acidification / proton motive force-driven plasma membrane ATP synthesis / sodium ion transport / phagocytic vesicle / proton-transporting ATPase activity, rotational mechanism / proton-transporting ATP synthase activity, rotational mechanism / lysosomal membrane / 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 | ![]() | 1.2 MB | Display | ![]() |
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PDB format | ![]() | Display | ![]() | |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
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-Validation report
Summary document | ![]() | 4 MB | Display | ![]() |
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Full document | ![]() | 4 MB | Display | |
Data in XML | ![]() | 206.4 KB | Display | |
Data in CIF | ![]() | 274.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8iguC ![]() 8igvC 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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1 | ![]()
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2 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 66059.547 Da / Num. of mol.: 6 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.: 6 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: Chemical | ChemComp-ADP / #4: Chemical | ChemComp-MG / Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.88 Å3/Da / Density % sol: 57.34 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop Details: 0.1M Tris-HCl (pH 8.5), 20% PEG 3350, 0.2M 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: Feb 12, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.1 Å / Relative weight: 1 |
Reflection | Resolution: 4.2→48.92 Å / Num. obs: 58670 / % possible obs: 99.9 % / Redundancy: 7.5 % / Biso Wilson estimate: 116.21 Å2 / CC1/2: 0.994 / Rmerge(I) obs: 0.24 / Rpim(I) all: 0.095 / Net I/σ(I): 7.2 |
Reflection shell | Resolution: 4.2→4.32 Å / Rmerge(I) obs: 1.07 / Mean I/σ(I) obs: 2.1 / Num. unique obs: 4576 / CC1/2: 0.764 / Rpim(I) all: 0.423 |
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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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 153.47 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 4.2→48.92 Å
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Refine LS restraints |
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LS refinement shell |
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