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Yorodumi- PDB-6s0m: Structural and dynamic studies provide insights into specificity ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6s0m | ||||||
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Title | Structural and dynamic studies provide insights into specificity and allosteric regulation of Ribonuclease AS, a key enzyme in mycobacterial virulence | ||||||
Components |
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Keywords | RNA BINDING PROTEIN / ---- | ||||||
Function / homology | Function and homology information RNA exonuclease activity / 3'-5' exonuclease activity / Hydrolases; Acting on ester bonds; Exoribonucleases producing 5'-phosphomonoesters / nucleic acid binding / magnesium ion binding Similarity search - Function | ||||||
Biological species | Mycobacterium tuberculosis (bacteria) Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2 Å | ||||||
Authors | Berisio, R. / Romano, M. | ||||||
Citation | Journal: J.Biomol.Struct.Dyn. / Year: 2020 Title: Structural and dynamic studies provide insights into specificity and allosteric regulation of ribonuclease as, a key enzyme in mycobacterial virulence. Authors: Calvanese, L. / Squeglia, F. / Romano, M. / D'Auria, G. / Falcigno, L. / Berisio, R. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6s0m.cif.gz | 89.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6s0m.ent.gz | 66.8 KB | Display | PDB format |
PDBx/mmJSON format | 6s0m.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6s0m_validation.pdf.gz | 2 MB | Display | wwPDB validaton report |
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Full document | 6s0m_full_validation.pdf.gz | 2 MB | Display | |
Data in XML | 6s0m_validation.xml.gz | 19.2 KB | Display | |
Data in CIF | 6s0m_validation.cif.gz | 28.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/s0/6s0m ftp://data.pdbj.org/pub/pdb/validation_reports/s0/6s0m | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 19546.061 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) Gene: DSI35_27935, ERS007661_00730, ERS007663_02388, ERS007665_04230, ERS007703_00653, ERS007722_01383, ERS007741_00970, ERS023446_01558, ERS027644_03090, ERS027651_00179, ERS027652_01481, ERS027653_ ...Gene: DSI35_27935, ERS007661_00730, ERS007663_02388, ERS007665_04230, ERS007703_00653, ERS007722_01383, ERS007741_00970, ERS023446_01558, ERS027644_03090, ERS027651_00179, ERS027652_01481, ERS027653_00165, ERS027654_01704, ERS027656_02031, ERS027661_01114, ERS027666_02618, ERS031537_02141, ERS124361_01165, SAMEA2682864_00498, SAMEA2683035_01322 Production host: Escherichia coli (E. coli) References: UniProt: A0A045JQ63, Hydrolases; Acting on ester bonds; Exoribonucleases producing 5'-phosphomonoesters #2: RNA chain | | Mass: 645.454 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Production host: Escherichia coli (E. coli) #3: Chemical | ChemComp-MG / #4: 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: 2.15 Å3/Da / Density % sol: 42.87 % |
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Crystal grow | Temperature: 277 K / Method: evaporation Details: protein concentration of 14 mg/mL in 0.1M HEPES pH 7.5, 10% w/v polyethylene glycol 8,000, 8% v/v ethylene glycol. Crystals of the complex of RNase AS with GMP were prepared by soaking ...Details: protein concentration of 14 mg/mL in 0.1M HEPES pH 7.5, 10% w/v polyethylene glycol 8,000, 8% v/v ethylene glycol. Crystals of the complex of RNase AS with GMP were prepared by soaking crystals of native protein in a solution containing GMP at 20 mM. |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ROTATING ANODE / Type: Cu FINE FOCUS / Wavelength: 1.54 Å |
Detector | Type: RIGAKU SATURN 944 / Detector: CCD / Date: Oct 10, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54 Å / Relative weight: 1 |
Reflection | Resolution: 2→30 Å / Num. obs: 23972 / % possible obs: 99.9 % / Redundancy: 6.9 % / Net I/σ(I): 20.2 |
Reflection shell | Resolution: 2→2.03 Å / Num. unique obs: 1170 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→30 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.919 / SU B: 4.463 / SU ML: 0.123 / Cross valid method: THROUGHOUT / ESU R: 0.209 / ESU R Free: 0.188 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 30.917 Å2
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Refinement step | Cycle: 1 / Resolution: 2→30 Å
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Refine LS restraints |
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