+Open data
-Basic information
Entry | Database: PDB / ID: 8sva | ||||||
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Title | Structure of the Rhodococcus sp. USK13 DarR-20 bp DNA complex | ||||||
Components |
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Keywords | TRANSCRIPTION/DNA / transcription / repressor / DarR / M. smegmatis / TetR / TFR / TRANSCRIPTION-DNA complex | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Rhodococcus sp. USK13 (bacteria) Rhodococcus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.96 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 | 8sva.cif.gz | 360.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8sva.ent.gz | 292 KB | Display | PDB format |
PDBx/mmJSON format | 8sva.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8sva_validation.pdf.gz | 758.2 KB | Display | wwPDB validaton report |
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Full document | 8sva_full_validation.pdf.gz | 785.8 KB | Display | |
Data in XML | 8sva_validation.xml.gz | 32.4 KB | Display | |
Data in CIF | 8sva_validation.cif.gz | 43.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/sv/8sva ftp://data.pdbj.org/pub/pdb/validation_reports/sv/8sva | HTTPS FTP |
-Related structure data
Related structure data | 8suaC 8sukC 8sv6C 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
#1: Protein | Mass: 23747.797 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Details: 100% match to NCBI Reference Sequence: WP_213575646.1 Source: (gene. exp.) Rhodococcus sp. USK13 (bacteria) / Gene: C5613_22450 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A2S8J6Y8 #2: DNA chain | Mass: 6132.991 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Rhodococcus (bacteria) #3: Chemical | ChemComp-PO4 / | #4: Water | ChemComp-HOH / | Has ligand of interest | Y | Sequence details | Entity 1 TetR/AcrR family transcriptional regulator is a 100% match to NCBI Reference Sequence: WP_213575646.1 | |
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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: 2.55 Å3/Da / Density % sol: 51.71 % |
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Crystal grow | Temperature: 278 K / Method: vapor diffusion, hanging drop Details: 0.1 M MES pH 6.5, 30% PEG 8000 and 0.1 M Calcium acetate |
-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: 0.989 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 3, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.989 Å / Relative weight: 1 |
Reflection | Resolution: 2.96→42.19 Å / Num. obs: 22523 / % possible obs: 99.7 % / Redundancy: 7.3 % / CC1/2: 0.998 / Rpim(I) all: 0.064 / Rsym value: 0.163 / Net I/σ(I): 8.9 |
Reflection shell | Resolution: 2.96→3.03 Å / Mean I/σ(I) obs: 0.5 / Num. unique obs: 1477 / CC1/2: 0.137 / Rpim(I) all: 1.575 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 2.96→42.19 Å / SU ML: 0.6 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 32.88 / 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: 2.96→42.19 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: -47.5104 Å / Origin y: -5.2229 Å / Origin z: 0.7496 Å
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Refinement TLS group | Selection details: all |