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Yorodumi- PDB-5a0v: Catalysis and 5' end sensing by ribonuclease RNase J of the metal... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5a0v | ||||||
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Title | Catalysis and 5' end sensing by ribonuclease RNase J of the metallo- beta-lactamase family | ||||||
Components |
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Keywords | HYDROLASE/RNA / HYDROLASE-RNA COMPLEX / ENDONUCLEASE / EXONUCLEASE | ||||||
Function / homology | Function and homology information 5'-3' RNA exonuclease activity / RNA endonuclease activity / rRNA processing / Hydrolases; Acting on ester bonds / RNA binding / zinc ion binding / cytoplasm Similarity search - Function | ||||||
Biological species | STREPTOMYCES COELICOLOR A3 | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å | ||||||
Authors | Pei, X.Y. / Bralley, P. / Jones, G.H. / Luisi, B.F. | ||||||
Citation | Journal: Nucleic Acids Res. / Year: 2015 Title: Linkage of Catalysis and 5' End Recognition in Ribonuclease Rnase J Authors: Pei, X.Y. / Bralley, P. / Jones, G.H. / Luisi, B.F. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5a0v.cif.gz | 385.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5a0v.ent.gz | 314.1 KB | Display | PDB format |
PDBx/mmJSON format | 5a0v.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5a0v_validation.pdf.gz | 774.2 KB | Display | wwPDB validaton report |
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Full document | 5a0v_full_validation.pdf.gz | 783.4 KB | Display | |
Data in XML | 5a0v_validation.xml.gz | 35.4 KB | Display | |
Data in CIF | 5a0v_validation.cif.gz | 48.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/a0/5a0v ftp://data.pdbj.org/pub/pdb/validation_reports/a0/5a0v | HTTPS FTP |
-Related structure data
Related structure data | 5a0tSC 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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2 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS oper: (Code: given Matrix: (0.2866, -0.000552, -0.9581), Vector: |
-Components
#1: Protein | Mass: 61146.090 Da / Num. of mol.: 2 Fragment: BETA-LACTAMASE DOMAIN AND BETA-CASP DOMAIN, RESIDUES 1-561 Source method: isolated from a genetically manipulated source Source: (gene. exp.) STREPTOMYCES COELICOLOR A3(2) (bacteria) Plasmid: PET19B / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): ROSETTA2 PLYSS / References: UniProt: O86842 #2: RNA chain | Mass: 1827.141 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) STREPTOMYCES COELICOLOR A3(2) (bacteria) Plasmid: PET19B / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): ROSETTA2 PLYSS #3: Chemical | ChemComp-ZN / #4: Chemical | ChemComp-C5P / | #5: 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: 4.9 Å3/Da / Density % sol: 0.74 % Description: DATA WERE COLLECTED USING THE OSCILLATION METHOD |
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Crystal grow | pH: 8.5 Details: THE BEST CRYSTALS OF S. COELICOLOR RNASE J WERE OBTAINED IN THE 27.5% W/V PEG 400, 0.1 M TRIS-HCL, PH 8.5 BY MIXING A 1:2 VOLUME RATIO OF CRYSTALLIZATION RESERVOIR TO PROTEIN SOLUTION, THEN SOAKED WITH MNCL2 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.91742 |
Detector | Type: DECTRIS PILATUS / Detector: PIXEL / Date: Feb 1, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.91742 Å / Relative weight: 1 |
Reflection | Resolution: 2.7→2.75 Å / Num. obs: 47608 / % possible obs: 99.8 % / Observed criterion σ(I): 2.5 / Redundancy: 6.9 % / Biso Wilson estimate: 55.49 Å2 / Rmerge(I) obs: 0.14 / Net I/σ(I): 9.7 |
Reflection shell | Resolution: 2.7→2.85 Å / Redundancy: 14.4 % / Rmerge(I) obs: 0.77 / Mean I/σ(I) obs: 2.5 / % possible all: 99.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 5A0T Resolution: 2.8→32.719 Å / SU ML: 0.32 / σ(F): 0.05 / Phase error: 20.92 / Stereochemistry target values: ML Details: DISORDERED REGIONS OF RESIDUES 456 TO 561 IN BOTH A CHAIN AND B CHAIN WERE NOT MODELLED.
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.8→32.719 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Origin x: 16.8119 Å / Origin y: 60.5149 Å / Origin z: -12.4589 Å
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Refinement TLS group | Selection details: ALL |