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Open data
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Basic information
Entry | Database: PDB / ID: 7dg7 | ||||||
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Title | DPBB domain of VCP-like ATPase from Methanopyrus kandleri | ||||||
![]() | ATPase of the AAA+ class | ||||||
![]() | CHAPERONE / Double psi beta barrel | ||||||
Function / homology | ![]() intein-mediated protein splicing / endonuclease activity / ATP hydrolysis activity / ATP binding 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 | ![]() | 33.1 KB | Display | ![]() |
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PDB format | ![]() | 20.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 434.7 KB | Display | ![]() |
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Full document | ![]() | 435.2 KB | Display | |
Data in XML | ![]() | 6.6 KB | Display | |
Data in CIF | ![]() | 8.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7dboC ![]() 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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Unit cell |
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Components
#1: Protein | Mass: 9993.531 Da / Num. of mol.: 1 / Fragment: DPBB domain Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Gene: MK0486 / Production host: ![]() ![]() | ||||||
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#2: Chemical | #3: Chemical | ChemComp-ZN / #4: Water | ChemComp-HOH / | Has ligand of interest | N | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 1.93 Å3/Da / Density % sol: 36.37 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop Details: 100mM imidazole/HCl pH7.8, 2M NaCl, 200mM Zinc acetate |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS3 S 2M / Detector: PIXEL / Date: Jun 21, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.6→50 Å / Num. obs: 10094 / % possible obs: 98.7 % / Redundancy: 13.2 % / CC1/2: 0.99 / Net I/σ(I): 22.97 |
Reflection shell | Resolution: 1.6→1.7 Å / Num. unique obs: 1569 / CC1/2: 0.979 |
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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: 61.6 Å2 / Biso mean: 20.4052 Å2 / Biso min: 3.87 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.604→40.436 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0
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