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Yorodumi- PDB-3h1c: Crystal structure of Polynucleotide Phosphorylase (PNPase) core b... -
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-Basic information
Entry | Database: PDB / ID: 3h1c | ||||||
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Title | Crystal structure of Polynucleotide Phosphorylase (PNPase) core bound to RNase E and Tungstate | ||||||
Components |
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Keywords | TRANSFERASE / polynucleotide phosphorylase / RNA turnover / Cytoplasm / Nucleotidyltransferase / RNA-binding / Stress response / Endonuclease / Hydrolase / Nuclease | ||||||
Function / homology | Function and homology information regulation of RNA helicase activity / ribonuclease E / rRNA 5'-end processing / ribonuclease E activity / polyribonucleotide nucleotidyltransferase / polyribonucleotide nucleotidyltransferase activity / bacterial degradosome / endoribonuclease complex / DEAD/H-box RNA helicase binding / cyclic-di-GMP binding ...regulation of RNA helicase activity / ribonuclease E / rRNA 5'-end processing / ribonuclease E activity / polyribonucleotide nucleotidyltransferase / polyribonucleotide nucleotidyltransferase activity / bacterial degradosome / endoribonuclease complex / DEAD/H-box RNA helicase binding / cyclic-di-GMP binding / 7S RNA binding / RNA catabolic process / tRNA processing / mRNA catabolic process / RNA processing / RNA nuclease activity / RNA endonuclease activity / cytoplasmic side of plasma membrane / rRNA processing / protein complex oligomerization / 3'-5'-RNA exonuclease activity / response to heat / protein homotetramerization / tRNA binding / molecular adaptor activity / rRNA binding / magnesium ion binding / RNA binding / zinc ion binding / membrane / identical protein binding / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.57 Å | ||||||
Authors | Nurmohamed, S. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2009 Title: Crystal structure of Escherichia coli polynucleotide phosphorylase core bound to RNase E, RNA and manganese: implications for catalytic mechanism and RNA degradosome assembly Authors: Nurmohamed, S. / Vaidialingam, B. / Callaghan, A.J. / 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 | 3h1c.cif.gz | 1.2 MB | Display | PDBx/mmCIF format |
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PDB format | pdb3h1c.ent.gz | 1021.8 KB | Display | PDB format |
PDBx/mmJSON format | 3h1c.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/h1/3h1c ftp://data.pdbj.org/pub/pdb/validation_reports/h1/3h1c | HTTPS FTP |
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-Related structure data
Related structure data | 3gcmSC 3gllC 3gmeC S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
-Components
#1: Protein | Mass: 59656.828 Da / Num. of mol.: 12 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: BL21 DE3 References: UniProt: P05055, polyribonucleotide nucleotidyltransferase #2: Protein/peptide | Mass: 4340.687 Da / Num. of mol.: 12 / Fragment: UNP residues 1021-1061 / Source method: obtained synthetically / Details: This sequence occurs naturally in E. coli / References: UniProt: P21513, ribonuclease E #3: Chemical | ChemComp-WO4 / |
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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: 3.79 Å3/Da / Density % sol: 67.56 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 4.5 Details: 0.2M ammonium hydrogen citrate, 17% PEG 3350, 50mM disodium tungstate, pH4.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.873 Å |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jul 15, 2006 / Details: Monochromator |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.873 Å / Relative weight: 1 |
Reflection | Resolution: 3.57→79.5 Å / Num. all: 129998 / Num. obs: 123425 / % possible obs: 94.2 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 2.8 % / Biso Wilson estimate: 57.1 Å2 / Rmerge(I) obs: 0.123 / Net I/σ(I): 11.4 |
Reflection shell | Resolution: 3.57→3.73 Å / Redundancy: 2.4 % / Rmerge(I) obs: 0.392 / Mean I/σ(I) obs: 2.3 / Num. unique all: 129998 / % possible all: 94.2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3GCM Resolution: 3.57→25 Å / Cross valid method: THROUGHOUT / σ(F): 2 / σ(I): 2
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Refinement step | Cycle: LAST / Resolution: 3.57→25 Å
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