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Yorodumi- PDB-6a4e: Two linked uridine bound Oligoribonuclease (ORN) from Colwellia p... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6a4e | ||||||
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Title | Two linked uridine bound Oligoribonuclease (ORN) from Colwellia psychrerythraea strain 34H | ||||||
Components |
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Keywords | HYDROLASE / Oligoribonuclease / Exonuclease / Colwellia psychrerythraea strain 34H | ||||||
Function / homology | Function and homology information Hydrolases; Acting on ester bonds; Exonucleases that are active with either ribo- or deoxyribonucleic acids and produce 5'-phosphomonoesters / DNA metabolic process / 3'-5'-RNA exonuclease activity / nucleic acid binding / cytoplasm Similarity search - Function | ||||||
Biological species | Colwellia psychrerythraea (bacteria) synthetic construct (others) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.45 Å | ||||||
Authors | Lee, C.W. / Park, S. / Lee, J.H. | ||||||
Citation | Journal: Sci Rep / Year: 2019 Title: Structural basis of small RNA hydrolysis by oligoribonuclease (CpsORN) from Colwellia psychrerythraea strain 34H. Authors: Lee, C.W. / Park, S.H. / Jeong, C.S. / Cha, S.S. / Park, H. / Lee, J.H. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6a4e.cif.gz | 86.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6a4e.ent.gz | 65 KB | Display | PDB format |
PDBx/mmJSON format | 6a4e.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/a4/6a4e ftp://data.pdbj.org/pub/pdb/validation_reports/a4/6a4e | 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
#1: Protein | Mass: 20578.461 Da / Num. of mol.: 2 / Mutation: D163A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Colwellia psychrerythraea (strain 34H / ATCC BAA-681) (bacteria) Strain: 34H / ATCC BAA-681 / Gene: orn, CPS_4379 / Production host: Escherichia coli (E. coli) References: UniProt: Q47VZ4, Hydrolases; Acting on ester bonds #2: RNA chain | Mass: 1485.872 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) #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: 2.75 Å3/Da / Density % sol: 55.28 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.4 Details: 0.04 M citric acid, 0.06 M Bis-Tris propane pH 6.4, 20% (w/v) PEG 3350 |
-Data collection
Diffraction | Mean temperature: 200 K |
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Diffraction source | Source: SYNCHROTRON / Site: PAL/PLS / Beamline: 5C (4A) / Wavelength: 0.9795 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 24, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 2.45→50 Å / Num. obs: 18200 / % possible obs: 96.2 % / Redundancy: 21.8 % / Net I/σ(I): 76.1 |
Reflection shell | Resolution: 2.45→2.49 Å |
-Processing
Software |
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Refinement | Resolution: 2.45→47.34 Å / SU ML: 0.28 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 31.45
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.45→47.34 Å
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Refine LS restraints |
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LS refinement shell |
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