+Open data
-Basic information
Entry | Database: PDB / ID: 8bpz | ||||||
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Title | Crystal structure of YopR | ||||||
Components | SPbeta prophage-derived uncharacterized protein YopR | ||||||
Keywords | DNA BINDING PROTEIN / yopR / phage-repressor / recombinase | ||||||
Function / homology | DNA breaking-rejoining enzyme, catalytic core / DNA binding / SPbeta prophage-derived uncharacterized protein YopR Function and homology information | ||||||
Biological species | Bacillus subtilis subsp. subtilis str. 168 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å | ||||||
Authors | Gallego del Sol, F. / Marina, A. | ||||||
Funding support | Spain, 1items
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Citation | Journal: Cell Host Microbe / Year: 2023 Title: Characterization of a unique repression system present in arbitrium phages of the SPbeta family. Authors: Brady, A. / Cabello-Yeves, E. / Gallego Del Sol, F. / Chmielowska, C. / Mancheno-Bonillo, J. / Zamora-Caballero, S. / Omer, S.B. / Torres-Puente, M. / Eldar, A. / Quiles-Puchalt, N. / Marina, A. / Penades, J.R. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8bpz.cif.gz | 148.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8bpz.ent.gz | 115.6 KB | Display | PDB format |
PDBx/mmJSON format | 8bpz.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bp/8bpz ftp://data.pdbj.org/pub/pdb/validation_reports/bp/8bpz | HTTPS FTP |
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-Related structure data
Related structure data | 8bj6C 8bjvSC S: Starting model for refinement 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: 37633.016 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacillus subtilis subsp. subtilis str. 168 (bacteria) Gene: yopR, BSU20790 / Production host: Escherichia coli (E. coli) / References: UniProt: O34558 |
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#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.46 Å3/Da / Density % sol: 50 % |
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Crystal grow | Temperature: 294 K / Method: vapor diffusion, sitting drop Details: 30.00 % w/v Polyethylene glycol 4,000, 100 mM tri-Sodium citrate; pH 5.6, 100 mM Ammonium sulfate3/D |
-Data collection
Diffraction | Mean temperature: 80 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.97934 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 5, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97934 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→94.47 Å / Num. obs: 19078 / % possible obs: 100 % / Redundancy: 18.9 % / CC1/2: 0.999 / Rpim(I) all: 0.018 / Rrim(I) all: 0.077 / Net I/σ(I): 23 / Num. measured all: 360632 |
Reflection shell | Resolution: 2.2→2.32 Å / % possible obs: 100 % / Redundancy: 20.1 % / Num. measured all: 55510 / Num. unique obs: 2767 / CC1/2: 0.985 / Rpim(I) all: 0.099 / Rrim(I) all: 0.445 / Net I/σ(I) obs: 7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 8BJV Resolution: 2.2→94.47 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.945 / SU B: 13.978 / SU ML: 0.183 / Cross valid method: THROUGHOUT / ESU R Free: 0.221 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 60.647 Å2
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Refinement step | Cycle: 1 / Resolution: 2.2→94.47 Å
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Refine LS restraints |
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