+Open data
-Basic information
Entry | Database: PDB / ID: 7dxx | ||||||
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Title | Crystal structure of the mk2h_deltaMILPS peptide homodimer | ||||||
Components | mk2h_deltaMILPS protein | ||||||
Keywords | CHAPERONE / Double psi beta barrel | ||||||
Function / homology | MALONIC ACID Function and homology information | ||||||
Biological species | synthetic construct (others) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.403 Å | ||||||
Authors | Yagi, S. / Tagami, S. | ||||||
Funding support | Japan, 1items
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Citation | Journal: J.Am.Chem.Soc. / Year: 2021 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: Journal: Biorxiv / Year: 2021 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7dxx.cif.gz | 51.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7dxx.ent.gz | 37.2 KB | Display | PDB format |
PDBx/mmJSON format | 7dxx.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dx/7dxx ftp://data.pdbj.org/pub/pdb/validation_reports/dx/7dxx | HTTPS FTP |
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-Related structure data
Related structure data | 7dboC 7dg7C 7dg9C 7di0C 7di1C 7du6C 7du7C 7dvcC 7dvfC 7dvhC 7dwwC 7dxrC 7dxsC 7dxtC 7dxuC 7dxvC 7dxwSC 7dxyC 7dxzC 7dycC S: Starting model for refinement C: citing same article (ref.) |
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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 on special symmetry positions |
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-Components
#1: Protein/peptide | Mass: 5286.242 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) synthetic construct (others) / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) #2: Chemical | ChemComp-MLA / | #3: Water | ChemComp-HOH / | Has ligand of interest | N | |
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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 Å3/Da / Density % sol: 38.42 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / Details: 2000 M Sodium malonate dibasic |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å |
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: 1.4→50 Å / Num. obs: 17646 / % possible obs: 99.3 % / Redundancy: 11.73 % / CC1/2: 0.999 / Net I/σ(I): 29.38 |
Reflection shell | Resolution: 1.4→1.49 Å / Num. unique obs: 2652 / CC1/2: 0.94 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 7DXW Resolution: 1.403→37.053 Å / SU ML: 0.13 / Cross valid method: THROUGHOUT / σ(F): 1.47 / Phase error: 19.98 / 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: 75.26 Å2 / Biso mean: 21.5126 Å2 / Biso min: 8.01 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.403→37.053 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0
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