+Open data
-Basic information
Entry | Database: PDB / ID: 7du7 | ||||||
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Title | Crystal structure of the rationally designed mkDPBB_sym1 protein | ||||||
Components | mkDPBB_sym1 protein | ||||||
Keywords | CHAPERONE / Double psi beta barrel | ||||||
Biological species | synthetic construct (others) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.201 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. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7du7.cif.gz | 83.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7du7.ent.gz | 63.4 KB | Display | PDB format |
PDBx/mmJSON format | 7du7.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7du7_validation.pdf.gz | 435.2 KB | Display | wwPDB validaton report |
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Full document | 7du7_full_validation.pdf.gz | 437.8 KB | Display | |
Data in XML | 7du7_validation.xml.gz | 10.2 KB | Display | |
Data in CIF | 7du7_validation.cif.gz | 13.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/du/7du7 ftp://data.pdbj.org/pub/pdb/validation_reports/du/7du7 | HTTPS FTP |
-Related structure data
Related structure data | 7dboC 7dg7C 7dg9C 7di0C 7di1C 7du6SC 7dvcC 7dvfC 7dvhC 7dwwC 7dxrC 7dxsC 7dxtC 7dxuC 7dxvC 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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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 9762.511 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) #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: 1.91 Å3/Da / Density % sol: 35.59 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / Details: 2100mM Maleic acid |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NW12A / Wavelength: 1 Å |
Detector | Type: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Nov 29, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.2→50 Å / Num. obs: 44946 / % possible obs: 99.7 % / Redundancy: 4.88 % / CC1/2: 0.999 / Net I/σ(I): 16.14 |
Reflection shell | Resolution: 1.2→1.27 Å / Num. unique obs: 7142 / CC1/2: 0.9915 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 7DU6 Resolution: 1.201→27.071 Å / SU ML: 0.13 / Cross valid method: THROUGHOUT / σ(F): 2.06 / Phase error: 26.18 / 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: 74.07 Å2 / Biso mean: 26.9676 Å2 / Biso min: 11.44 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.201→27.071 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0
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