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Open data
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Basic information
Entry | Database: PDB / ID: 7dbo | ||||||
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Title | DPBB domain of VCP-like ATPase from Thermoplasma acidophilum | ||||||
![]() | VCP-like ATPase | ||||||
![]() | CHAPERONE / Double psi beta barrel | ||||||
Function / homology | ![]() retrograde protein transport, ER to cytosol / polyubiquitin modification-dependent protein binding / ATP hydrolysis activity / ATP binding / cytosol Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Yagi, S. / Tagami, S. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Seven Amino Acid Types Suffice to Create the Core Fold of RNA Polymerase. Authors: Yagi, S. / Padhi, A.K. / Vucinic, J. / Barbe, S. / Schiex, T. / Nakagawa, R. / Simoncini, D. / Zhang, K.Y.J. / Tagami, S. #1: ![]() Title: Seven amino acid types suffice to reconstruct the core fold of RNA polymerase Authors: Yagi, S. / Padhi, A.K. / Vucinic, J. / Barbe, S. / Schiex, T. / Nakagawa, R. / Simoncini, D. / Zhang, K.Y.J. / Tagami, S. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 47.4 KB | Display | ![]() |
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PDB format | ![]() | 37.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 7dg7C ![]() 7dg9C ![]() 7di0C ![]() 7di1C ![]() 7du6C ![]() 7du7C ![]() 7dvcC ![]() 7dvfC ![]() 7dvhC ![]() 7dwwC ![]() 7dxrC ![]() 7dxsC ![]() 7dxtC ![]() 7dxuC ![]() 7dxvC ![]() 7dxwC ![]() 7dxxC ![]() 7dxyC ![]() 7dxzC ![]() 7dycC C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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2 | ![]()
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Unit cell |
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Components on special symmetry positions |
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Components
#1: Protein | Mass: 10509.551 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Gene: vat, Ta0840 / Production host: ![]() ![]() #2: Chemical | ChemComp-SO4 / #3: Water | ChemComp-HOH / | Has ligand of interest | N | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.23 Å3/Da / Density % sol: 44.92 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop Details: 100mM citrate / phosphate pH5.0, 1.4M Ammonium sulfate |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: RAYONIX MX225-HS / Detector: CCD / Date: Feb 5, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→50 Å / Num. obs: 14642 / % possible obs: 99.7 % / Redundancy: 22.1 % / CC1/2: 0.995 / Rsym value: 0.114 / Net I/σ(I): 7.69 |
Reflection shell | Resolution: 1.9→2.02 Å / Mean I/σ(I) obs: 1.21 / Num. unique obs: 2292 / CC1/2: 0.615 / Rsym value: 1.331 |
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Processing
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Refinement | Method to determine structure: ![]()
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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 max: 107.5 Å2 / Biso mean: 38.0305 Å2 / Biso min: 12.58 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.9→41.07 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 10
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