+Open data
-Basic information
Entry | Database: PDB / ID: 6n6f | ||||||
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Title | Vibrio cholerae Oligoribonuclease bound to pGC | ||||||
Components |
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Keywords | rna binding protein/rna / 3'-5' exoribonuclease / RNA BINDING PROTEIN / rna binding protein-rna complex | ||||||
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 / 3'-5'-RNA exonuclease activity / nucleic acid binding / Hydrolases; Acting on ester bonds / cytoplasm Similarity search - Function | ||||||
Biological species | Vibrio cholerae (bacteria) synthetic construct (others) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.735 Å | ||||||
Authors | Lormand, J.D. / Sondermann, H. | ||||||
Funding support | United States, 1items
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Citation | Journal: Elife / Year: 2019 Title: A dedicated diribonucleotidase resolves a key bottleneck for the terminal step of RNA degradation. Authors: Kim, S.K. / Lormand, J.D. / Weiss, C.A. / Eger, K.A. / Turdiev, H. / Turdiev, A. / Winkler, W.C. / Sondermann, H. / Lee, V.T. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6n6f.cif.gz | 99 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6n6f.ent.gz | 72 KB | Display | PDB format |
PDBx/mmJSON format | 6n6f.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6n6f_validation.pdf.gz | 433.3 KB | Display | wwPDB validaton report |
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Full document | 6n6f_full_validation.pdf.gz | 433.3 KB | Display | |
Data in XML | 6n6f_validation.xml.gz | 11.3 KB | Display | |
Data in CIF | 6n6f_validation.cif.gz | 16.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/n6/6n6f ftp://data.pdbj.org/pub/pdb/validation_reports/n6/6n6f | HTTPS FTP |
-Related structure data
Related structure data | 6n6aSC 6n6cC 6n6dC 6n6eC 6n6gC 6n6hC 6n6iC 6n6jC 6n6kC 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 on special symmetry positions |
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-Components
#1: Protein | Mass: 20954.910 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Vibrio cholerae (bacteria) / Gene: orn / Plasmid: pET28a / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21DE3 References: UniProt: A0A0H6V4D7, UniProt: Q9KV17*PLUS, Hydrolases; Acting on ester bonds |
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#2: RNA chain | Mass: 605.430 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
#3: Chemical | ChemComp-NA / |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.15 Å3/Da / Density % sol: 60.95 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.5 Details: 0.1 M BisTris (pH 5.5), 17% polyethylene glycol 3350, and 20% xylitol |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: CHESS / Beamline: F1 / Wavelength: 0.977 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 14, 2018 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: Si(111) crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.977 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.735→47.18 Å / Num. all: 28405 / Num. obs: 28405 / % possible obs: 99.8 % / Redundancy: 11.9 % / Rpim(I) all: 0.016 / Rrim(I) all: 0.056 / Rsym value: 0.054 / Net I/av σ(I): 9.6 / Net I/σ(I): 24 / Num. measured all: 338345 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6N6A Resolution: 1.735→32.317 Å / SU ML: 0.17 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 17.67
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 95.51 Å2 / Biso mean: 36.3173 Å2 / Biso min: 21.06 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.735→32.317 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 10
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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