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Yorodumi- PDB-4aim: Crystal structure of C. crescentus PNPase bound to RNase E recogn... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4aim | ||||||
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Title | Crystal structure of C. crescentus PNPase bound to RNase E recognition peptide | ||||||
Components |
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Keywords | TRANSFERASE/PEPTIDE / TRANSFERASE-PEPTIDE COMPLEX / KH DOMAIN / S1 DOMAIN / GWW PEPTIDE | ||||||
Function / homology | Function and homology information ribonuclease E / polyribonucleotide nucleotidyltransferase / polyribonucleotide nucleotidyltransferase activity / ribonuclease E activity / tRNA processing / mRNA catabolic process / RNA processing / RNA endonuclease activity / cytoplasmic side of plasma membrane / rRNA processing ...ribonuclease E / polyribonucleotide nucleotidyltransferase / polyribonucleotide nucleotidyltransferase activity / ribonuclease E activity / tRNA processing / mRNA catabolic process / RNA processing / RNA endonuclease activity / cytoplasmic side of plasma membrane / rRNA processing / 3'-5'-RNA exonuclease activity / tRNA binding / rRNA binding / magnesium ion binding / RNA binding / zinc ion binding / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | CAULOBACTER VIBRIOIDES (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.3 Å | ||||||
Authors | Hardwick, S.W. / Gubbey, T. / Hug, I. / Jenal, U. / Luisi, B.F. | ||||||
Citation | Journal: Open Biol. / Year: 2012 Title: Crystal Structure of Caulobacter Crescentus Polynucleotide Phosphorylase Reveals a Mechanism of RNA Substrate Channelling and RNA Degradosome Assembly. Authors: Hardwick, S.W. / Gubbey, T. / Hug, I. / Jenal, U. / 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 | 4aim.cif.gz | 157.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4aim.ent.gz | 119.5 KB | Display | PDB format |
PDBx/mmJSON format | 4aim.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4aim_validation.pdf.gz | 450.7 KB | Display | wwPDB validaton report |
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Full document | 4aim_full_validation.pdf.gz | 487.5 KB | Display | |
Data in XML | 4aim_validation.xml.gz | 30.8 KB | Display | |
Data in CIF | 4aim_validation.cif.gz | 41.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ai/4aim ftp://data.pdbj.org/pub/pdb/validation_reports/ai/4aim | HTTPS FTP |
-Related structure data
Related structure data | 4aidC 4am3C 3gmeS C: citing same article (ref.) S: Starting model for refinement |
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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
#1: Protein | Mass: 78145.383 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) CAULOBACTER VIBRIOIDES (bacteria) / Strain: CB15 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) References: UniProt: Q9AC32, polyribonucleotide nucleotidyltransferase |
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#2: Protein/peptide | Mass: 1798.081 Da / Num. of mol.: 1 / Fragment: PNPASE BINDING PEPTIDE - GWW, RESIDUES 885-898 / Source method: obtained synthetically / Source: (synth.) CAULOBACTER VIBRIOIDES (bacteria) / References: UniProt: Q9A749 |
#3: Chemical | ChemComp-PO4 / |
#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: 3.28 Å3/Da / Density % sol: 62.52 % / Description: NONE |
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Crystal grow | Details: 17 % WT/V PEG 3000, 0.1 M TRI-SODIUM CITRATE |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.9778 |
Detector | Type: MARRESEARCH MX-300 / Detector: CCD / Date: Oct 14, 2010 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9778 Å / Relative weight: 1 |
Reflection | Resolution: 3.3→40 Å / Num. obs: 15391 / % possible obs: 99.3 % / Observed criterion σ(I): 2 / Redundancy: 4.7 % / Rmerge(I) obs: 0.14 / Net I/σ(I): 7.8 |
Reflection shell | Resolution: 3.3→3.48 Å / Redundancy: 4.6 % / Rmerge(I) obs: 0.65 / Mean I/σ(I) obs: 2.4 / % possible all: 99.2 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3GME Resolution: 3.3→38.73 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.906 / SU B: 25.049 / SU ML: 0.42 / Cross valid method: THROUGHOUT / ESU R Free: 0.51 / 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: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 96.546 Å2
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Refinement step | Cycle: LAST / Resolution: 3.3→38.73 Å
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Refine LS restraints |
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