+Open data
-Basic information
Entry | Database: PDB / ID: 7t8l | |||||||||||||||
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Title | BrxR from Acinetobacter BREX type I phage restriction system | |||||||||||||||
Components | BrxR | |||||||||||||||
Keywords | DNA BINDING PROTEIN / Phage restriction / BREX / DNA binding / regulatory / Acinetobacter / Bacteriophage Exclusion | |||||||||||||||
Function / homology | WYL domain protein, s026 type / WYL domain / WYL domain / WYL domain-containing protein Function and homology information | |||||||||||||||
Biological species | Acinetobacter sp. NEB 394 (bacteria) | |||||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2 Å | |||||||||||||||
Authors | Doyle, L. / Kaiser, B. / Stoddard, B. | |||||||||||||||
Funding support | United States, 4items
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Citation | Journal: Nucleic Acids Res. / Year: 2022 Title: Identification and characterization of the WYL BrxR protein and its gene as separable regulatory elements of a BREX phage restriction system. Authors: Luyten, Y.A. / Hausman, D.E. / Young, J.C. / Doyle, L.A. / Higashi, K.M. / Ubilla-Rodriguez, N.C. / Lambert, A.R. / Arroyo, C.S. / Forsberg, K.J. / Morgan, R.D. / Stoddard, B.L. / Kaiser, B.K. | |||||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7t8l.cif.gz | 226.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7t8l.ent.gz | 185.8 KB | Display | PDB format |
PDBx/mmJSON format | 7t8l.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7t8l_validation.pdf.gz | 450.1 KB | Display | wwPDB validaton report |
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Full document | 7t8l_full_validation.pdf.gz | 453.2 KB | Display | |
Data in XML | 7t8l_validation.xml.gz | 23.2 KB | Display | |
Data in CIF | 7t8l_validation.cif.gz | 32.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/t8/7t8l ftp://data.pdbj.org/pub/pdb/validation_reports/t8/7t8l | HTTPS FTP |
-Related structure data
Related structure data | 7t8kC 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: 33807.469 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Details: The protein was expressed and crystallized with only Cysteines, however some of those Cysteines were converted to S-Sulfinocysteines (CSD) due to treatment of the crystals with Hydrogen ...Details: The protein was expressed and crystallized with only Cysteines, however some of those Cysteines were converted to S-Sulfinocysteines (CSD) due to treatment of the crystals with Hydrogen peroxide (supported by very clear electron density). The CSD are only a byproduct of H2O2 treatment during freezing, not originally in the expressed/crystallized protein. Source: (gene. exp.) Acinetobacter sp. NEB 394 (bacteria) / Gene: HUK62_18310 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A7H8SL41 #2: Chemical | ChemComp-EDO / #3: Chemical | ChemComp-CL / | #4: Water | ChemComp-HOH / | Has ligand of interest | N | |
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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: 2.23 Å3/Da / Density % sol: 44.93 % |
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Crystal grow | Temperature: 300 K / Method: vapor diffusion, hanging drop / pH: 7.3 / Details: 10%PEG3000 / 0.1 M Hepes, pH 7.3 / 2% Benz-HCL |
-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: 0.97918 Å | |||||||||||||||||||||
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: May 20, 2020 | |||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||
Radiation wavelength | Wavelength: 0.97918 Å / Relative weight: 1 | |||||||||||||||||||||
Reflection | Resolution: 2→63.92 Å / Num. obs: 40089 / % possible obs: 99.5 % / Redundancy: 3 % / CC1/2: 0.985 / Rmerge(I) obs: 0.078 / Rpim(I) all: 0.074 / Rrim(I) all: 0.108 / Net I/σ(I): 6.9 | |||||||||||||||||||||
Reflection shell | Diffraction-ID: 1 / Redundancy: 2.8 %
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-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 2→63.92 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.93 / SU B: 4.385 / SU ML: 0.122 / Cross valid method: FREE R-VALUE / ESU R: 0.187 / ESU R Free: 0.169 Details: Hydrogens have been added in their riding positions
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 30.848 Å2
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Refinement step | Cycle: LAST / Resolution: 2→63.92 Å
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Refine LS restraints |
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LS refinement shell |
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