+Open data
-Basic information
Entry | Database: PDB / ID: 8suk | ||||||
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Title | Structure of Rhodococcus sp. USK13 DarR-c-di-AMP complex | ||||||
Components |
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Keywords | TRANSCRIPTION / TFR / Mycobacteria | ||||||
Function / homology | DNA Function and homology information | ||||||
Biological species | Rhodococcus sp. USK13 (bacteria) synthetic construct (others) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.45 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 | 8suk.cif.gz | 328.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8suk.ent.gz | 266.3 KB | Display | PDB format |
PDBx/mmJSON format | 8suk.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8suk_validation.pdf.gz | 2.2 MB | Display | wwPDB validaton report |
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Full document | 8suk_full_validation.pdf.gz | 2.2 MB | Display | |
Data in XML | 8suk_validation.xml.gz | 30.9 KB | Display | |
Data in CIF | 8suk_validation.cif.gz | 43.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/su/8suk ftp://data.pdbj.org/pub/pdb/validation_reports/su/8suk | HTTPS FTP |
-Related structure data
Related structure data | 8suaC 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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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 23466.424 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rhodococcus sp. USK13 (bacteria) / Production host: Escherichia coli (E. coli) #2: DNA chain | Mass: 581.456 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) #3: Chemical | ChemComp-SO4 / #4: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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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: 2.9 Å3/Da / Density % sol: 57.57 % |
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Crystal grow | Temperature: 274 K / Method: vapor diffusion, hanging drop Details: 0.1 M Tris pH 8.5, 1.34 M lithium sulphate and 1.3% PEG 400 |
-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 PILATUS3 6M / Detector: PIXEL / Date: Jan 12, 2023 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.45→41.49 Å / Num. obs: 40140 / % possible obs: 98 % / Redundancy: 3.2 % / CC1/2: 0.989 / Rpim(I) all: 0.07 / Rsym value: 0.107 / Net I/σ(I): 5.8 |
Reflection shell | Resolution: 2.45→2.52 Å / Mean I/σ(I) obs: 1.1 / Num. unique obs: 2175 / CC1/2: 0.654 / Rpim(I) all: 0.378 / Rsym value: 0.538 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.45→41.49 Å / SU ML: 0.39 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 27.59 / 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: 2.45→41.49 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: 32.0161 Å / Origin y: -9.2999 Å / Origin z: 58.5224 Å
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Refinement TLS group | Selection details: all |