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- PDB-2xdb: A processed non-coding RNA regulates a bacterial antiviral system -
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Open data
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Basic information
Entry | Database: PDB / ID: 2xdb | ||||||
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Title | A processed non-coding RNA regulates a bacterial antiviral system | ||||||
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![]() | TOXIN/RNA / TOXIN-RNA COMPLEX / ABORTIVE INFECTION / PHAGE | ||||||
Function / homology | ![]() plasmid maintenance / RNA endonuclease activity / defense response to virus / Hydrolases; Acting on ester bonds / negative regulation of DNA-templated transcription / RNA binding / identical protein binding Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Blower, T.R. / Pei, X.Y. / Short, F.L. / Fineran, P.C. / Humphreys, D.P. / Luisi, B.F. / Salmond, G.P.C. | ||||||
![]() | ![]() Title: A Processed Noncoding RNA Regulates an Altruistic Bacterial Antiviral System. Authors: Blower, T.R. / Pei, X.Y. / Short, F.L. / Fineran, P.C. / Humphreys, D.P. / Luisi, B.F. / Salmond, G.P.C. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 128.7 KB | Display | ![]() |
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PDB format | ![]() | 98.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 474.7 KB | Display | ![]() |
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Full document | ![]() | 479.7 KB | Display | |
Data in XML | ![]() | 11.8 KB | Display | |
Data in CIF | ![]() | 15.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2xd0C ![]() 2xddS C: citing same article ( 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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Components on special symmetry positions |
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Components
#1: Protein | Mass: 19726.537 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() | ||||||
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#2: RNA chain | Mass: 12822.509 Da / Num. of mol.: 1 / Fragment: BACTERIA ANTITOX, RESIDUES 1775-1814 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() | ||||||
#3: Chemical | ChemComp-SO4 / #4: Chemical | ChemComp-CO / #5: Water | ChemComp-HOH / | Nonpolymer details | A23: RNA IS CLEAVED BY TOXN (CHAIN A IN THE STRUCTURE) AT A-32, AND FORMING 2'3'-CYCLOPHOSP | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.7 Å3/Da / Density % sol: 0.55 % / Description: NONE |
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Crystal grow | pH: 6.5 / Details: 0.01M COCL2, 0.1M MES PH6.5, 1.8M (NH4)2SO4 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC CCD / Detector: CCD / Date: Jul 8, 2009 / Details: SINGLE SILICON (111) MONOCHROMATOR |
Radiation | Monochromator: DOUBLE CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9702 Å / Relative weight: 1 |
Reflection | Resolution: 2.55→75 Å / Num. obs: 18604 / % possible obs: 100 % / Observed criterion σ(I): 3 / Redundancy: 20 % / Biso Wilson estimate: 62.05 Å2 / Rmerge(I) obs: 0.15 / Net I/σ(I): 13.9 |
Reflection shell | Resolution: 2.5→2.55 Å / Redundancy: 20.7 % / Rmerge(I) obs: 0.78 / Mean I/σ(I) obs: 1.7 / % possible all: 99.5 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 2XDD Resolution: 2.55→45.91 Å / SU ML: 0.47 / σ(F): 1.52 / Phase error: 22.56 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 75.43 Å2 / ksol: 0.38 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 73.9 Å2
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Refinement step | Cycle: LAST / Resolution: 2.55→45.91 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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