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Yorodumi- PDB-7coq: Hexameric Ring Complex of Engineered V1-ATPase bound to AMP-PNP: ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7coq | ||||||||||||
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Title | Hexameric Ring Complex of Engineered V1-ATPase bound to AMP-PNP: A3(De)3_(ANP)1cat | ||||||||||||
Components |
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Keywords | MOTOR PROTEIN / Computational Design / Rotary Molecular Motor / Protein Complex | ||||||||||||
Function / homology | Function and homology information Na+-transporting two-sector ATPase / sodium-transporting ATP synthase activity, rotational mechanism / sodium-transporting ATPase activity, rotational mechanism / proton-transporting ATP synthase complex / proton motive force-driven plasma membrane ATP synthesis / sodium ion transport / proton-transporting ATPase activity, rotational mechanism / proton-transporting ATP synthase activity, rotational mechanism / ATP binding Similarity search - Function | ||||||||||||
Biological species | Enterococcus hirae ATCC 9790 (bacteria) | ||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.44 Å | ||||||||||||
Authors | Kosugi, T. / Tanabe, M. / Koga, N. | ||||||||||||
Funding support | Japan, 3items
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Citation | Journal: To Be Published Title: De Novo Design of Allosteric Control into Rotary Motor V1-ATPase by Restoring Lost Function Authors: Kosugi, T. / Iida, T. / Tanabe, M. / Iino, R. / Koga, N. | ||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7coq.cif.gz | 595.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7coq.ent.gz | 485.8 KB | Display | PDB format |
PDBx/mmJSON format | 7coq.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/co/7coq ftp://data.pdbj.org/pub/pdb/validation_reports/co/7coq | HTTPS FTP |
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-Related structure data
Related structure data | 7cop 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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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.) Enterococcus hirae ATCC 9790 (bacteria) Strain: ATCC 9790 / Gene: ntpA, EHR_08260 / Production host: Escherichia coli (E. coli) 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.) Enterococcus hirae ATCC 9790 (bacteria) Strain: ATCC 9790 / Gene: ntpB, EHR_08265 / Production host: Escherichia coli (E. coli) / References: UniProt: Q08637 #3: Chemical | ChemComp-MG / | #4: Chemical | ChemComp-ANP / | Has ligand of interest | Y | |
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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: 2.97 Å3/Da / Density % sol: 58.52 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop Details: 0.1 M Tris-HCl (pH 8.5), 22% PEG 3350 and 0.4 M Ammonium Acetate |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: BL-1A / Wavelength: 1.1 Å |
Detector | Type: DECTRIS EIGER X 4M / Detector: PIXEL / Date: Apr 30, 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: 3.44→46.34 Å / Num. obs: 53244 / % possible obs: 99.8 % / Redundancy: 6.9 % / Rmerge(I) obs: 0.117 / Net I/σ(I): 11.3 |
Reflection shell | Resolution: 3.44→3.55 Å / Redundancy: 6.8 % / Rmerge(I) obs: 0.845 / Mean I/σ(I) obs: 2.4 / Num. unique obs: 4602 / % possible all: 99.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 7COP 7cop Resolution: 3.44→46.34 Å / SU ML: 0.46 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 27.06 / Stereochemistry target values: ML
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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: 3.44→46.34 Å
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Refine LS restraints |
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LS refinement shell |
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