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Yorodumi- PDB-4ba2: Archaeal exosome (Rrp4-Rrp41(D182A)-Rrp42) bound to inorganic pho... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4ba2 | ||||||
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Title | Archaeal exosome (Rrp4-Rrp41(D182A)-Rrp42) bound to inorganic phosphate | ||||||
Components |
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Keywords | HYDROLASE/RNA / HYDROLASE-RNA COMPLEX / ARCHAEA / RNA DEGRADATION / PHOSPHOROLYTIC REACTION MECHANISM | ||||||
Function / homology | Function and homology information cytoplasmic exosome (RNase complex) / CUT catabolic process / U4 snRNA 3'-end processing / poly(A)-dependent snoRNA 3'-end processing / exosome (RNase complex) / exonucleolytic trimming to generate mature 3'-end of 5.8S rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / : / rRNA catabolic process / poly(A) binding / Hydrolases; Acting on ester bonds; Exoribonucleases producing 5'-phosphomonoesters ...cytoplasmic exosome (RNase complex) / CUT catabolic process / U4 snRNA 3'-end processing / poly(A)-dependent snoRNA 3'-end processing / exosome (RNase complex) / exonucleolytic trimming to generate mature 3'-end of 5.8S rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / : / rRNA catabolic process / poly(A) binding / Hydrolases; Acting on ester bonds; Exoribonucleases producing 5'-phosphomonoesters / 3'-5'-RNA exonuclease activity / RNA binding / cytoplasm Similarity search - Function | ||||||
Biological species | SULFOLOBUS SOLFATARICUS (archaea) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.501 Å | ||||||
Authors | Lorentzen, E. / Conti, E. | ||||||
Citation | Journal: Archaea / Year: 2012 Title: Crystal Structure of a 9-Subunit Archaeal Exosome in Pre-Catalytic States of the Phosphorolytic Reaction. Authors: Lorentzen, E. / Conti, E. | ||||||
History |
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Remark 700 | SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "IC" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "IC" 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 | 4ba2.cif.gz | 300 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4ba2.ent.gz | 241.1 KB | Display | PDB format |
PDBx/mmJSON format | 4ba2.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ba/4ba2 ftp://data.pdbj.org/pub/pdb/validation_reports/ba/4ba2 | HTTPS FTP |
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-Related structure data
Related structure data | 4ba1C 2je6S 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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Unit cell |
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Components on special symmetry positions |
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-Components
-PROBABLE EXOSOME COMPLEX EXONUCLEASE ... , 2 types, 2 molecules AB
#1: Protein | Mass: 30422.824 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) SULFOLOBUS SOLFATARICUS (archaea) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): K-12 / References: UniProt: Q9UXC0 |
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#2: Protein | Mass: 27764.125 Da / Num. of mol.: 1 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) SULFOLOBUS SOLFATARICUS (archaea) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): K-12 / References: UniProt: Q9UXC2 |
-Protein / RNA chain , 2 types, 2 molecules IR
#3: Protein | Mass: 28225.320 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) SULFOLOBUS SOLFATARICUS (archaea) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): K-12 / References: UniProt: Q9UXC4 |
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#4: RNA chain | Mass: 1271.866 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) SULFOLOBUS SOLFATARICUS (archaea) |
-Non-polymers , 4 types, 109 molecules
#5: Chemical | ChemComp-1PE / | ||||
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#6: Chemical | #7: Chemical | ChemComp-NA / | #8: Water | ChemComp-HOH / | |
-Details
Sequence details | D182A MUTATION |
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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: 2.6 Å3/Da / Density % sol: 52 % / Description: NONE |
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Crystal grow | pH: 8 / Details: 40% PEG 400, 50 MM TRIS-HCL PH 8.0 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.97995 |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Jan 29, 2007 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97995 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→50 Å / Num. obs: 28497 / % possible obs: 1 % / Observed criterion σ(I): -2 / Redundancy: 7.1 % / Rmerge(I) obs: 0.12 / Net I/σ(I): 14.5 |
Reflection shell | Resolution: 2.5→2.65 Å / Redundancy: 7.1 % / Rmerge(I) obs: 0.72 / Mean I/σ(I) obs: 2.9 / % possible all: 1 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2JE6 Resolution: 2.501→38.922 Å / SU ML: 0.42 / σ(F): 1.38 / Phase error: 27.89 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.501→38.922 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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