+Open data
-Basic information
Entry | Database: PDB / ID: 7f37 | |||||||||||||||
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Title | Crystal structure of AtaT2-AtaR2 complex | |||||||||||||||
Components |
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Keywords | TRANSFERASE / Acetyltransferase / TOXIN | |||||||||||||||
Function / homology | : / : Function and homology information | |||||||||||||||
Biological species | Escherichia coli O157:H7 (bacteria) | |||||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.896 Å | |||||||||||||||
Authors | Yashiro, Y. / Tomita, K. | |||||||||||||||
Funding support | Japan, 4items
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Citation | Journal: Cell Rep / Year: 2021 Title: Molecular basis of glycyl-tRNAGly acetylation by TacT from Salmonella Typhimurium Authors: Yashiro, Y. / Zhang, C. / Sakaguchi, Y. / Suzuki, T. / Tomita, K. | |||||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7f37.cif.gz | 138.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7f37.ent.gz | 108.1 KB | Display | PDB format |
PDBx/mmJSON format | 7f37.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7f37_validation.pdf.gz | 478.7 KB | Display | wwPDB validaton report |
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Full document | 7f37_full_validation.pdf.gz | 501.3 KB | Display | |
Data in XML | 7f37_validation.xml.gz | 26.2 KB | Display | |
Data in CIF | 7f37_validation.cif.gz | 35.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/f3/7f37 ftp://data.pdbj.org/pub/pdb/validation_reports/f3/7f37 | HTTPS FTP |
-Related structure data
Related structure data | 7f36C 5fvjS 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 | Mass: 18741.707 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli O157:H7 (bacteria) Gene: Z4777, CQJ22_000873, E3157_02175, E3158_02185, E5F07_24590, FDZ86_02175 Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A7U8MJD7 #2: Protein | Mass: 10433.930 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli O157:H7 (bacteria) Gene: CQJ22_000874, E3157_02180, E3158_02190, E3175_02180, E5F07_24585, FDZ86_02180 Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A7U8MLT5 #3: 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: 2.5 Å3/Da / Density % sol: 50.85 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.2M Potassium formate, 20% PEG 3350 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: BL-17A / Wavelength: 0.98 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 2, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 |
Reflection | Resolution: 2.896→46.12 Å / Num. obs: 17558 / % possible obs: 99.9 % / Redundancy: 13.4 % / CC1/2: 0.993 / Rmerge(I) obs: 0.28 / Net I/σ(I): 7.5 |
Reflection shell | Resolution: 2.9→3 Å / Rmerge(I) obs: 1.92 / Mean I/σ(I) obs: 1.4 / Num. unique obs: 1708 / CC1/2: 0.76 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5fvj Resolution: 2.896→45.375 Å / SU ML: 0.41 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 30.3 / Stereochemistry target values: ML Details: The reflection data set was anisotropically truncated and corrected using UCLA-DOE LAB Diffraction Anisotropy Server, and used for the refinement. Also, PDB extract was run using the ...Details: The reflection data set was anisotropically truncated and corrected using UCLA-DOE LAB Diffraction Anisotropy Server, and used for the refinement. Also, PDB extract was run using the anisotropically processed structure factor (.mtz) file.
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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: 105.73 Å2 / Biso mean: 37.6895 Å2 / Biso min: 3.85 Å2 | ||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.896→45.375 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0
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