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- PDB-7dxy: Crystal structure of the chemically synthesized mk2h_deltaMILPS p... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7dxy | ||||||
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Title | Crystal structure of the chemically synthesized mk2h_deltaMILPS peptide homodimer | ||||||
![]() | mk2h_deltaMILPS | ||||||
![]() | CHAPERONE / Double psi beta barrel | ||||||
Biological species | synthetic construct (others) | ||||||
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 | ![]() | 46.5 KB | Display | ![]() |
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PDB format | ![]() | 33.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 428.1 KB | Display | ![]() |
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Full document | ![]() | 428.4 KB | Display | |
Data in XML | ![]() | 6.7 KB | Display | |
Data in CIF | ![]() | 8.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7dboC ![]() 7dg7C ![]() 7dg9C ![]() 7di0C ![]() 7di1C ![]() 7du6C ![]() 7du7C ![]() 7dvcC ![]() 7dvfC ![]() 7dvhC ![]() 7dwwC ![]() 7dxrC ![]() 7dxsC ![]() 7dxtC ![]() 7dxuC ![]() 7dxvC ![]() 7dxwC ![]() 7dxxSC ![]() 7dxzC ![]() 7dycC S: Starting model for refinement 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/peptide | Mass: 4846.713 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) synthetic construct (others) / Production host: ![]() ![]() #2: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.02 Å3/Da / Density % sol: 39.03 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop Details: 400mM Sodium phosphate monobasic/1600mM Pottasium phosphate dibasic, 100 mM imidazole_HCl, pH 8.0, 200 mM NaCl |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Sep 11, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.35→50 Å / Num. obs: 17566 / % possible obs: 99.2 % / Redundancy: 6.26 % / CC1/2: 1 / Net I/σ(I): 18.85 |
Reflection shell | Resolution: 1.35→1.44 Å / Num. unique obs: 2759 / CC1/2: 0.832 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 7DXX Resolution: 1.4→24.263 Å / SU ML: 0.13 / Cross valid method: THROUGHOUT / σ(F): 1.47 / Phase error: 29.15 / 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 98.94 Å2 / Biso mean: 31.1788 Å2 / Biso min: 16.93 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.4→24.263 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0
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