+Open data
-Basic information
Entry | Database: PDB / ID: 7u02 | ||||||
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Title | Structure of the C. crescentus DriD C-domain bound to ssDNA | ||||||
Components |
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Keywords | TRANSCRIPTION / DriD / DNA repair / SOS-independent repair / DidA | ||||||
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 / SAD / molecular replacement / Resolution: 2.48 Å | ||||||
Authors | Schumacher, M.A. | ||||||
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 | 7u02.cif.gz | 171.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7u02.ent.gz | 134.3 KB | Display | PDB format |
PDBx/mmJSON format | 7u02.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7u02_validation.pdf.gz | 1.1 MB | Display | wwPDB validaton report |
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Full document | 7u02_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 7u02_validation.xml.gz | 17 KB | Display | |
Data in CIF | 7u02_validation.cif.gz | 22.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/u0/7u02 ftp://data.pdbj.org/pub/pdb/validation_reports/u0/7u02 | HTTPS FTP |
-Related structure data
Related structure data | 7tzvC 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: 21750.715 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Caulobacter vibrioides (strain ATCC 19089 / CB15) (bacteria) Strain: ATCC 19089 / CB15 / Gene: CC_1095 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9A999 #2: DNA chain | | Mass: 886.637 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) #3: Chemical | #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: 3.47 Å3/Da / Density % sol: 64.53 % |
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Crystal grow | Temperature: 297 K / Method: vapor diffusion, hanging drop / Details: Ammonium sulphate |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 5.0.1 / Wavelength: 1.01 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Feb 4, 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: 2.45→66.6 Å / Num. obs: 43538 / % possible obs: 99.9 % / Redundancy: 7.9 % / CC1/2: 1 / Rpim(I) all: 0.033 / Rsym value: 0.089 / Net I/σ(I): 15 |
Reflection shell | Resolution: 2.45→2.49 Å / Mean I/σ(I) obs: 0.7 / Num. unique obs: 1977 / CC1/2: 0.334 / Rpim(I) all: 1.034 / Rsym value: 2.89 |
-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 2.48→66.54 Å / SU ML: 0.42 / Cross valid method: THROUGHOUT / σ(F): 0.06 / Phase error: 36 / 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: 242.07 Å2 / Biso mean: 117.7346 Å2 / Biso min: 49.83 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.48→66.54 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 22
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Refinement TLS params. | Method: refined / Origin x: -3.5975 Å / Origin y: 44.0495 Å / Origin z: 58.5775 Å
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Refinement TLS group |
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