+Open data
-Basic information
Entry | Database: PDB / ID: 8sua | ||||||
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Title | Structure of M. baixiangningiae DarR-ligand complex | ||||||
Components | DarR | ||||||
Keywords | TRANSCRIPTION / DarR / mycobacteria / TFR / TetR / c-di-AMP | ||||||
Function / homology | Chem-YT9 Function and homology information | ||||||
Biological species | Mycobacteriaceae (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.6 Å | ||||||
Authors | Schumacher, M.A. | ||||||
Funding support | United States, 1items
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Citation | Journal: Nat Commun / Year: 2023 Title: Structures of the DarR transcription regulator reveal unique modes of second messenger and DNA binding. Authors: Schumacher, M.A. / Lent, N. / Chen, V.B. / Salinas, R. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8sua.cif.gz | 128.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8sua.ent.gz | 101.8 KB | Display | PDB format |
PDBx/mmJSON format | 8sua.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8sua_validation.pdf.gz | 734.1 KB | Display | wwPDB validaton report |
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Full document | 8sua_full_validation.pdf.gz | 734.7 KB | Display | |
Data in XML | 8sua_validation.xml.gz | 11.1 KB | Display | |
Data in CIF | 8sua_validation.cif.gz | 16 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/su/8sua ftp://data.pdbj.org/pub/pdb/validation_reports/su/8sua | HTTPS FTP |
-Related structure data
Related structure data | 8sukC 8sv6C 8svaC 8svdC 8t5yC C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-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 | Mass: 23484.424 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mycobacteriaceae (bacteria) / Production host: Escherichia coli (E. coli) |
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#2: Chemical | ChemComp-YT9 / |
#3: Water | ChemComp-HOH / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.8 Å3/Da / Density % sol: 56.09 % |
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Crystal grow | Temperature: 273 K / Method: vapor diffusion, hanging drop / Details: 1.5 M NaCl, 0.2 M MgCl2, 0.1 M Tris |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 3, 2022 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.6→47.72 Å / Num. obs: 35029 / % possible obs: 99.9 % / Redundancy: 11.2 % / CC1/2: 1 / Rpim(I) all: 0.02 / Rsym value: 0.047 / Net I/σ(I): 25.2 |
Reflection shell | Resolution: 1.6→1.64 Å / Mean I/σ(I) obs: 2.1 / Num. unique obs: 2647 / CC1/2: 0.805 / Rpim(I) all: 0.406 / Rsym value: 0.503 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 1.6→47.72 Å / SU ML: 0.15 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 20.41 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.6→47.72 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Origin x: 30.8114 Å / Origin y: 41.4852 Å / Origin z: 19.8965 Å
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Refinement TLS group | Selection details: all |