+Open data
-Basic information
Entry | Database: PDB / ID: 7dxv | ||||||
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Title | Crystal structure of the mk2h_deltaY peptide homodimer | ||||||
Components | mk2h_dY protein | ||||||
Keywords | CHAPERONE / Double psi beta barrel | ||||||
Biological species | synthetic construct (others) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.301 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 | 7dxv.cif.gz | 28.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7dxv.ent.gz | 18.9 KB | Display | PDB format |
PDBx/mmJSON format | 7dxv.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7dxv_validation.pdf.gz | 436.5 KB | Display | wwPDB validaton report |
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Full document | 7dxv_full_validation.pdf.gz | 437.8 KB | Display | |
Data in XML | 7dxv_validation.xml.gz | 5.9 KB | Display | |
Data in CIF | 7dxv_validation.cif.gz | 7.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dx/7dxv ftp://data.pdbj.org/pub/pdb/validation_reports/dx/7dxv | HTTPS FTP |
-Related structure data
Related structure data | 7dboC 7dg7C 7dg9C 7di0C 7di1C 7du6C 7du7C 7dvcC 7dvfC 7dvhC 7dwwC 7dxrSC 7dxsC 7dxtC 7dxuC 7dxwC 7dxxC 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: 5126.074 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: 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: 2.47 Å3/Da / Density % sol: 50.13 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / Details: 100 mM SPG buffer, 25 % PEG 1500 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B2 / Wavelength: 1 Å |
Detector | Type: RAYONIX MX225-HS / Detector: CCD / Date: Jul 22, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.21→50 Å / Num. obs: 4833 / % possible obs: 98 % / Redundancy: 10.87 % / CC1/2: 0.999 / Net I/σ(I): 29.72 |
Reflection shell | Resolution: 2.21→2.34 Å / Num. unique obs: 705 / CC1/2: 0.993 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 7DXR Resolution: 2.301→36.551 Å / SU ML: 0.34 / Cross valid method: THROUGHOUT / σ(F): 2.33 / Phase error: 30.72 / 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: 81.95 Å2 / Biso mean: 41.5106 Å2 / Biso min: 15.35 Å2 | ||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.301→36.551 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / % reflection obs: 100 %
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