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Open data
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Basic information
Entry | Database: PDB / ID: 3imq | ||||||
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Title | Crystal structure of the NusB101-S10(delta loop) complex | ||||||
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![]() | transcription regulator / ribosomal protein / Processive transcription antitermination / transcription termination / ![]() ![]() ![]() ![]() ![]() ![]() ![]() | ||||||
Function / homology | ![]() transcription antitermination factor activity, RNA binding / transcription elongation factor complex / regulation of DNA-templated transcription elongation / transcription antitermination / DNA-templated transcription termination / ![]() ![]() ![]() ![]() ![]() ![]() ![]() Similarity search - Function | ||||||
Biological species | ![]() ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Luo, X. / Wahl, M.C. | ||||||
![]() | ![]() Title: Fine tuning of the E. coli NusB:NusE complex affinity to BoxA RNA is required for processive antitermination. Authors: Burmann, B.M. / Luo, X. / Rosch, P. / Wahl, M.C. / Gottesman, M.E. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 143.5 KB | Display | ![]() |
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PDB format | ![]() | 114.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 3d3bS 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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1 | ![]()
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2 | ![]()
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3 | ![]()
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Unit cell |
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Details | The biological assembly is the hetero-dimer. There are three biological assemblies per asymmetric unit: A-J, B-K, C-L. |
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Components
#1: Protein | Mass: 15837.110 Da / Num. of mol.: 3 / Mutation: D118N Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() ![]() #2: Protein | ![]() Mass: 9608.144 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() ![]() #3: Chemical | ChemComp-K / | #4: Water | ChemComp-HOH / | ![]() Sequence details | THE LOOP KERFTVLISPHVNKDARDQYEI IN UNP REFERENCE P0A7R5 WAS DELETED IN CONSTRUCT AND REPLACED WITH ...THE LOOP KERFTVLISP | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.73 Å3/Da / Density % sol: 55.01 % |
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Crystal grow![]() | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 0.2 M potassium citrate, 20 % PEG 3350, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jul 7, 2008 / Details: mirrors |
Radiation | Monochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 2.5→30 Å / Num. all: 29761 / Num. obs: 29761 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.2 % / Biso Wilson estimate: 52.7 Å2 / Rsym value: 0.086 / Net I/σ(I): 18.1 |
Reflection shell | Resolution: 2.5→2.6 Å / Redundancy: 7.4 % / Mean I/σ(I) obs: 4.1 / Num. unique all: 3263 / Rsym value: 0.725 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure![]() ![]() Starting model: PDB entry 3D3B Resolution: 2.5→30 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.918 / SU B: 21.044 / SU ML: 0.215 / TLS residual ADP flag: LIKELY RESIDUAL / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / ESU R: 0.482 / ESU R Free: 0.286 / 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: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 21.621 Å2
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Refinement step | Cycle: LAST / Resolution: 2.5→30 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.5→2.564 Å / Total num. of bins used: 20
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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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