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Open data
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Basic information
Entry | Database: PDB / ID: 8bjv | ||||||
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Title | Crystal structure of YopR | ||||||
![]() | SPbeta prophage-derived uncharacterized protein YopR | ||||||
![]() | DNA BINDING PROTEIN / yopR / phage-repressor / recombinase | ||||||
Function / homology | DNA breaking-rejoining enzyme, catalytic core / DNA binding / SPbeta prophage-derived uncharacterized protein YopR![]() | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Gallego del Sol, F. / Marina, A. | ||||||
Funding support | ![]()
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![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 390.1 KB | Display | ![]() |
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PDB format | ![]() | 321.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 453.7 KB | Display | ![]() |
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Full document | ![]() | 460.1 KB | Display | |
Data in XML | ![]() | 35.5 KB | Display | |
Data in CIF | ![]() | 50.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8bj6C ![]() 8bpzC ![]() 8b6jS S: Starting model for refinement C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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3 | ![]()
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
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Components
#1: Protein | Mass: 37633.016 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Strain: 168 / Gene: yopR, BSU20790 / Production host: ![]() ![]() #2: Chemical | #3: Water | ChemComp-HOH / | Has ligand of interest | N | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.35 Å3/Da / Density % sol: 47.56 % |
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Crystal grow | Temperature: 294 K / Method: vapor diffusion, sitting drop Details: 20 % w/v Polyethylene glycol 6,000 100 mM tri-Sodium citrate; pH 5.0 |
-Data collection
Diffraction | Mean temperature: 80 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 5, 2022 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97926 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→93.22 Å / Num. obs: 50520 / % possible obs: 95.6 % / Redundancy: 6.1 % / CC1/2: 0.999 / Rpim(I) all: 0.03 / Rrim(I) all: 0.077 / Net I/σ(I): 13.8 / Num. measured all: 306236 |
Reflection shell | Resolution: 2.2→2.32 Å / % possible obs: 75.6 % / Redundancy: 3.8 % / Num. measured all: 21760 / Num. unique obs: 5767 / CC1/2: 0.816 / Rpim(I) all: 0.323 / Rrim(I) all: 0.648 / Net I/σ(I) obs: 1.9 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 8B6J Resolution: 2.2→93.22 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.93 / SU B: 17.138 / SU ML: 0.21 / Cross valid method: THROUGHOUT / ESU R: 0.369 / ESU R Free: 0.242 / 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: 51.751 Å2
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Refinement step | Cycle: 1 / Resolution: 2.2→93.22 Å
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Refine LS restraints |
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