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Yorodumi- PDB-7dxy: Crystal structure of the chemically synthesized mk2h_deltaMILPS p... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7dxy | ||||||
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Title | Crystal structure of the chemically synthesized mk2h_deltaMILPS peptide homodimer | ||||||
Components | mk2h_deltaMILPS | ||||||
Keywords | CHAPERONE / Double psi beta barrel | ||||||
Biological species | synthetic construct (others) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 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 | 7dxy.cif.gz | 46.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7dxy.ent.gz | 33.8 KB | Display | PDB format |
PDBx/mmJSON format | 7dxy.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7dxy_validation.pdf.gz | 428.1 KB | Display | wwPDB validaton report |
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Full document | 7dxy_full_validation.pdf.gz | 428.4 KB | Display | |
Data in XML | 7dxy_validation.xml.gz | 6.7 KB | Display | |
Data in CIF | 7dxy_validation.cif.gz | 8.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dx/7dxy ftp://data.pdbj.org/pub/pdb/validation_reports/dx/7dxy | 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 (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
#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: Escherichia coli (E. coli) #2: Water | ChemComp-HOH / | |
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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: 2.02 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: 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: 1.35→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 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT 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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