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Yorodumi- PDB-8jsk: Crystal structure of an N-terminal cyclic nucleotide-binding doma... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8jsk | ||||||
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Title | Crystal structure of an N-terminal cyclic nucleotide-binding domain of a PycTIR from Pseudovibrio sp. in complex with cUMP | ||||||
Components | PycTIR | ||||||
Keywords | SIGNALING PROTEIN / cUMP receptor / Pycsar effector protein | ||||||
Function / homology | Uridine-3',5'-cyclic monophosphate Function and homology information | ||||||
Biological species | Pseudovibrio sp. W64 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.401 Å | ||||||
Authors | Wang, Y.-C. / Yang, C.-S. / Hou, M.-H. / Chen, Y. | ||||||
Funding support | Taiwan, 1items
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Citation | Journal: Nat Commun / Year: 2024 Title: Structural and functional characterization of cyclic pyrimidine-regulated anti-phage system. Authors: Hou, M.H. / Chen, C.J. / Yang, C.S. / Wang, Y.C. / Chen, Y. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8jsk.cif.gz | 79.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8jsk.ent.gz | 57.1 KB | Display | PDB format |
PDBx/mmJSON format | 8jsk.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/js/8jsk ftp://data.pdbj.org/pub/pdb/validation_reports/js/8jsk | HTTPS FTP |
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-Related structure data
Related structure data | 8jsfC 8jsjC 8jszC 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: 17846.410 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Details: NCBI: KZK76288.1; cloning site: L151, E152 Tag: H153-H158 Source: (gene. exp.) Pseudovibrio sp. W64 (bacteria) / Production host: Escherichia coli BL21(DE3) (bacteria) #2: Chemical | ChemComp-6SY / | #3: 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: 2.13 Å3/Da / Density % sol: 42.14 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop Details: 0.075 M HEPES pH 7.5, 7.5% w/v polyethylene glycol 8,000, 6% v/v ethylene glycol and 25% v/v glycerol |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: NSRRC / Beamline: TPS 07A / Wavelength: 0.97626 Å |
Detector | Type: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Sep 21, 2022 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97626 Å / Relative weight: 1 |
Reflection | Resolution: 2.401→30 Å / Num. obs: 12049 / % possible obs: 99.8 % / Redundancy: 10.5 % / CC1/2: 1 / Net I/σ(I): 23.6 |
Reflection shell | Resolution: 2.41→2.5 Å / Redundancy: 11 % / Mean I/σ(I) obs: 2.7 / Num. unique obs: 1192 / CC1/2: 0.808 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: AlphaFold Resolution: 2.401→25.082 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.916 / SU B: 10.073 / SU ML: 0.23 / Cross valid method: THROUGHOUT / ESU R: 0.844 / ESU R Free: 0.288 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: 37.905 Å2
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Refinement step | Cycle: LAST / Resolution: 2.401→25.082 Å
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Refine LS restraints |
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LS refinement shell |
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