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- PDB-2wnr: The structure of Methanothermobacter thermautotrophicus exosome c... -
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Open data
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Basic information
Entry | Database: PDB / ID: 2wnr | ||||||
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Title | The structure of Methanothermobacter thermautotrophicus exosome core assembly | ||||||
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![]() | HYDROLASE / PHOSPHATE BINDING / 3'-5' EXORIBONUCLEASE / EXOSOME / NUCLEASE / EXONUCLEASE | ||||||
Function / homology | ![]() exosome (RNase complex) / RNA catabolic process / Hydrolases; Acting on ester bonds; Exoribonucleases producing 5'-phosphomonoesters / 3'-5'-RNA exonuclease activity / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Ng, C.L. / Waterman, D.G. / Antson, A.A. / Ortiz-Lombardia, M. | ||||||
![]() | ![]() Title: Structure of the Methanothermobacter Thermautotrophicus Exosome Rnase Ph Ring Authors: Ng, C.L. / Waterman, D.G. / Antson, A.A. / Ortiz-Lombardia, M. | ||||||
History |
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Remark 700 | THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE ... THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED. |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 275.8 KB | Display | ![]() |
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PDB format | ![]() | 222.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 483 KB | Display | ![]() |
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Full document | ![]() | 503.8 KB | Display | |
Data in XML | ![]() | 49.6 KB | Display | |
Data in CIF | ![]() | 68.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2br2S S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments:
NCS ensembles :
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Components
#1: Protein | Mass: 29924.561 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Strain: DELTA H / Plasmid: PCDFDUET, PET28A / Production host: ![]() ![]() References: UniProt: O26778, Hydrolases; Acting on ester bonds; Exoribonucleases producing 5'-phosphomonoesters #2: Protein | Mass: 26560.438 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Strain: DELTA H / Plasmid: PCDFDUET, PET28A / Production host: ![]() ![]() References: UniProt: O26779, Hydrolases; Acting on ester bonds; Exoribonucleases producing 5'-phosphomonoesters #3: Chemical | #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.45 Å3/Da / Density % sol: 49 % / Description: NONE |
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Crystal grow | pH: 7 Details: 20% PEG3350, 0.1M SUCCINIC ACID PH 7.0, 5% ISOPROPANOL |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Sep 25, 2005 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9191 Å / Relative weight: 1 |
Reflection | Resolution: 2.65→25 Å / Num. obs: 47654 / % possible obs: 98.7 % / Observed criterion σ(I): 1.5 / Redundancy: 4.2 % / Biso Wilson estimate: 64 Å2 / Rmerge(I) obs: 0.12 / Net I/σ(I): 9.1 |
Reflection shell | Resolution: 2.65→2.79 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.58 / Mean I/σ(I) obs: 1.5 / % possible all: 92.4 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 2BR2 Resolution: 2.65→24.86 Å / Cor.coef. Fo:Fc: 0.936 / Cor.coef. Fo:Fc free: 0.913 / SU B: 31.794 / SU ML: 0.298 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 1.231 / ESU R Free: 0.327 / 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: 1.4 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 65.2 Å2
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Refinement step | Cycle: LAST / Resolution: 2.65→24.86 Å
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Refine LS restraints |
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