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Yorodumi- PDB-7otr: Crystal structure of a psychrophilic CCA-adding enzyme determined... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7otr | |||||||||
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Title | Crystal structure of a psychrophilic CCA-adding enzyme determined by SAD phasing | |||||||||
Components | CCA-adding protein | |||||||||
Keywords | RNA BINDING PROTEIN / tRNA maturation / tRNA nucleotidyltransferase / psychrophilic enzyme | |||||||||
Function / homology | Function and homology information RNA 3'-end processing / tRNA processing / nucleotidyltransferase activity / nucleotide binding / RNA binding / metal ion binding Similarity search - Function | |||||||||
Biological species | Planococcus halocryophilus (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.25 Å | |||||||||
Authors | Rollet, K. / de Wijn, R. / Rios-Santacruz, R. / Hennig, O. / Betat, H. / Moerl, M. / Sauter, C. | |||||||||
Funding support | France, 2items
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Citation | Journal: Comput Struct Biotechnol J / Year: 2021 Title: CCA-addition in the cold: Structural characterization of the psychrophilic CCA-adding enzyme from the permafrost bacterium Planococcus halocryophilus . Authors: de Wijn, R. / Rollet, K. / Ernst, F.G.M. / Wellner, K. / Betat, H. / Morl, M. / Sauter, C. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7otr.cif.gz | 176.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7otr.ent.gz | 138 KB | Display | PDB format |
PDBx/mmJSON format | 7otr.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ot/7otr ftp://data.pdbj.org/pub/pdb/validation_reports/ot/7otr | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 48636.410 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Planococcus halocryophilus (bacteria) / Gene: BBI08_05760 / Plasmid: pET-30b(+) / Details (production host): pET-30bEk/LIC / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A1C7DQ98 |
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-Non-polymers , 5 types, 155 molecules
#2: Chemical | #3: Chemical | #4: Chemical | #5: Chemical | ChemComp-TRS / | #6: Water | ChemComp-HOH / | |
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-Details
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: 3.66 Å3/Da / Density % sol: 66.35 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop Details: protein solution at 4.5 mg/mL in 50 mM Tris-HCl pH 7.5, 200 mM NaCl, 5 mM MgCl2; reservoir solution: 100 mM Sodium acetate; pH 4.5 1 M di-Ammonium hydrogen phosphate PH range: 4.5 - 7.5 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 2.0751 Å |
Detector | Type: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Feb 28, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 2.0751 Å / Relative weight: 1 |
Reflection | Resolution: 2.25→50 Å / Num. obs: 64470 / % possible obs: 99 % / Redundancy: 78 % / Biso Wilson estimate: 44.74 Å2 / CC1/2: 0.999 / Rrim(I) all: 0.17 / Net I/σ(I): 30.7 |
Reflection shell | Resolution: 2.25→2.31 Å / Redundancy: 25 % / Num. unique obs: 4607 / CC1/2: 0.425 / Rrim(I) all: 3.11 / % possible all: 96.2 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 2.25→49.35 Å / SU ML: 0.2998 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 23.2544 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: 47.74 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.25→49.35 Å
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Refine LS restraints |
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LS refinement shell |
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