+Open data
-Basic information
Entry | Database: PDB / ID: 7tzv | ||||||
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Title | Structure of DriD C-domain bound to 9mer ssDNA | ||||||
Components |
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Keywords | TRANSCRIPTION / DriD / DNA repair / SOS-independent / WYL domain / wHTH | ||||||
Function / homology | Protein PafC / WYL domain / WYL domain / DNA / WYL domain-containing protein Function and homology information | ||||||
Biological species | Caulobacter vibrioides (bacteria) synthetic construct (others) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.65 Å | ||||||
Authors | Schumacher, M.A. / Laub, M. | ||||||
Funding support | United States, 1items
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Citation | Journal: Genes Dev. / Year: 2022 Title: ssDNA is an allosteric regulator of the C. crescentus SOS-independent DNA damage response transcription activator, DriD. Authors: Gozzi, K. / Salinas, R. / Nguyen, V.D. / Laub, M.T. / Schumacher, M.A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7tzv.cif.gz | 194.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7tzv.ent.gz | 151.6 KB | Display | PDB format |
PDBx/mmJSON format | 7tzv.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7tzv_validation.pdf.gz | 434.8 KB | Display | wwPDB validaton report |
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Full document | 7tzv_full_validation.pdf.gz | 437.8 KB | Display | |
Data in XML | 7tzv_validation.xml.gz | 21.4 KB | Display | |
Data in CIF | 7tzv_validation.cif.gz | 32.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/tz/7tzv ftp://data.pdbj.org/pub/pdb/validation_reports/tz/7tzv | HTTPS FTP |
-Related structure data
Related structure data | 7u02C 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: 22032.994 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Caulobacter vibrioides (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: Q9A999 #2: DNA chain | | Mass: 2705.797 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) #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: 2.47 Å3/Da / Density % sol: 50.2 % |
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Crystal grow | Temperature: 297 K / Method: vapor diffusion, hanging drop / Details: 0.1 M MES pH 6.5, 0.1 M Imidazole, 20% PEG 8000 |
-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: 1.01 Å |
Detector | Type: DECTRIS EIGER2 S 4M / Detector: PIXEL / Date: Dec 2, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.01 Å / Relative weight: 1 |
Reflection | Resolution: 1.65→36.1 Å / Num. obs: 55422 / % possible obs: 98.1 % / Redundancy: 5.9 % / CC1/2: 0.999 / Rpim(I) all: 0.029 / Rsym value: 0.049 / Net I/σ(I): 16.1 |
Reflection shell | Resolution: 1.65→1.69 Å / Mean I/σ(I) obs: 1.2 / Num. unique obs: 3432 / CC1/2: 0.886 / Rpim(I) all: 0.978 / Rsym value: 1.245 |
-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: DriD Cdomain, p3121 form Resolution: 1.65→31.49 Å / SU ML: 0.18 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 25.39 / 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: 88.17 Å2 / Biso mean: 37.8593 Å2 / Biso min: 17.1 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.65→31.49 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14
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Refinement TLS params. | Method: refined / Origin x: -16.0599 Å / Origin y: 2.1979 Å / Origin z: -8.0916 Å
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Refinement TLS group |
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