+Open data
-Basic information
Entry | Database: PDB / ID: 2bx2 | ||||||
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Title | Catalytic domain of E. coli RNase E | ||||||
Components |
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Keywords | HYDROLASE / RNA-BINDING / RNA TURNOVER / RNA PROCESSING / ENDONUCLEASE / NUCLEASE | ||||||
Function / homology | Function and homology information regulation of RNA helicase activity / ribonuclease E / rRNA 5'-end processing / ribonuclease E activity / bacterial degradosome / endoribonuclease complex / DEAD/H-box RNA helicase binding / 7S RNA binding / RNA catabolic process / tRNA processing ...regulation of RNA helicase activity / ribonuclease E / rRNA 5'-end processing / ribonuclease E activity / bacterial degradosome / endoribonuclease complex / DEAD/H-box RNA helicase binding / 7S RNA binding / RNA catabolic process / tRNA processing / mRNA catabolic process / RNA nuclease activity / RNA processing / RNA endonuclease activity / cytoplasmic side of plasma membrane / rRNA processing / protein complex oligomerization / protein homotetramerization / tRNA binding / rRNA binding / molecular adaptor activity / magnesium ion binding / RNA binding / zinc ion binding / membrane / identical protein binding / cytoplasm Similarity search - Function | ||||||
Biological species | ESCHERICHIA COLI (E. coli) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.85 Å | ||||||
Authors | Marcaida, M.J. / Callaghan, A.J. / Scott, W.G. / Luisi, B.F. | ||||||
Citation | Journal: Nature / Year: 2005 Title: Structure of E. Coli Rnase E Catalytic Domain and Implications for RNA Processing and Turnover Authors: Callaghan, A.J. / Marcaida, M.J. / Stead, J.A. / Mcdowall, K.J. / Scott, W.G. / Luisi, B.F. | ||||||
History |
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Remark 700 | SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "LB" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "LB" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 5-STRANDED BARREL THIS IS REPRESENTED BY A 6-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2bx2.cif.gz | 115.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2bx2.ent.gz | 93.3 KB | Display | PDB format |
PDBx/mmJSON format | 2bx2.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bx/2bx2 ftp://data.pdbj.org/pub/pdb/validation_reports/bx/2bx2 | 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 on special symmetry positions |
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Details | THE OLIGOMERIC STRUCTURE PREDICTED FOR THIS STRUCTUREIS A DIMER OF DIMERS. |
-Components
#1: Protein | Mass: 58215.133 Da / Num. of mol.: 1 / Fragment: CATALYTIC DOMAIN, RESIDUES 1-510 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ESCHERICHIA COLI (E. coli) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) References: UniProt: P21513, Hydrolases; Acting on ester bonds; Phosphoric-diester hydrolases | ||||||
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#2: RNA chain | Mass: 4693.746 Da / Num. of mol.: 1 / Source method: obtained synthetically | ||||||
#3: Chemical | #4: Chemical | ChemComp-ZN / | #5: Water | ChemComp-HOH / | Compound details | HAS A ROLE IN THE MATURATION | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 6.6 Å3/Da / Density % sol: 82 % |
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Crystal grow | pH: 8 Details: CRYSTALS OF THE RNASE E CATALYTIC DOMAIN/ RNA COMPLEX APPEARED AFTER TWO TO FOUR WEEKS IN 5 TO 20 % WT/V POLYETHYLENE GLYCOL 8,000, 0.1 M TRIS PH 7.5 TO 8.0, AND 10 TO 50 MM MAGNESIUM FORMATE AT 20OC |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.97 |
Detector | Type: MARRESEARCH / Detector: CCD |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97 Å / Relative weight: 1 |
Reflection | Resolution: 2.9→25 Å / Num. obs: 36133 / % possible obs: 97.4 % / Observed criterion σ(I): 2 / Redundancy: 9.2 % / Rmerge(I) obs: 0.1 / Net I/σ(I): 17.9 |
Reflection shell | Resolution: 2.85→3 Å / Redundancy: 9 % / Rmerge(I) obs: 0.81 / Mean I/σ(I) obs: 3.5 / % possible all: 96.7 |
-Processing
Software |
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Refinement | Method to determine structure: MAD / Resolution: 2.85→25 Å / Cor.coef. Fo:Fc: 0.935 / Cor.coef. Fo:Fc free: 0.914 / SU B: 20.488 / SU ML: 0.192 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.31 / ESU R Free: 0.254 / Stereochemistry target values: MAXIMUM LIKELIHOOD / 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: 1.2 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 56.15 Å2
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Refinement step | Cycle: LAST / Resolution: 2.85→25 Å
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