+Open data
-Basic information
Entry | Database: PDB / ID: 7n10 | ||||||
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Title | Co-crystal structure of Prx with ComR DNA binding domain | ||||||
Components |
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Keywords | VIRAL PROTEIN/TRANSCRIPTION / paratox / ComR / Streptococcus / bacteriophage / quorum sensing / natural competence / VIRAL PROTEIN-TRANSCRIPTION complex | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Streptococcus pyogenes serotype M3 (bacteria) Streptococcus mutans serotype c (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.65 Å | ||||||
Authors | Rutbeek, N.R. / Prehna, G. | ||||||
Funding support | Canada, 1items
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Citation | Journal: J.Biol.Chem. / Year: 2021 Title: Molecular mechanism of quorum sensing inhibition in Streptococcus by the phage protein paratox. Authors: Rutbeek, N.R. / Rezasoltani, H. / Patel, T.R. / Khajehpour, M. / Prehna, G. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7n10.cif.gz | 113.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7n10.ent.gz | 72.6 KB | Display | PDB format |
PDBx/mmJSON format | 7n10.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/n1/7n10 ftp://data.pdbj.org/pub/pdb/validation_reports/n1/7n10 | HTTPS FTP |
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-Related structure data
Related structure data | 7n1nC 6ckaS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 8095.225 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Details: Cloning artifact Source: (gene. exp.) Streptococcus pyogenes serotype M3 (strain ATCC BAA-595 / MGAS315) (bacteria) Strain: ATCC BAA-595 / MGAS315 / Gene: SpyM3_1300 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A0H2UWN8 #2: Protein | | Mass: 7578.767 Da / Num. of mol.: 1 / Fragment: DNA binding domain (UNP residues 1-66) Source method: isolated from a genetically manipulated source Source: (gene. exp.) Streptococcus mutans serotype c (strain ATCC 700610 / UA159) (bacteria) Strain: ATCC 700610 / UA159 / Gene: SMU_61 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q8DWI6 #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: 1.53 Å3/Da / Density % sol: 19.6 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop Details: 15 mg/mL protein, 20% PEG3500, 0.2 M potassium acetate |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.28329 Å |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Oct 21, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.28329 Å / Relative weight: 1 |
Reflection | Resolution: 1.65→45 Å / Num. obs: 18234 / % possible obs: 99.9 % / Redundancy: 6.1 % / Biso Wilson estimate: 24.69 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.067 / Rpim(I) all: 0.027 / Net I/σ(I): 15.2 |
Reflection shell | Resolution: 1.65→1.68 Å / Redundancy: 6.1 % / Rmerge(I) obs: 0.727 / Mean I/σ(I) obs: 2.3 / Num. unique obs: 918 / CC1/2: 0.867 / Rpim(I) all: 0.316 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 6CKA Resolution: 1.65→45 Å / SU ML: 0.2101 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 21.9961 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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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 mean: 31.74 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.65→45 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group | Refine-ID: X-RAY DIFFRACTION
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