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- PDB-4kb4: Crystal structure of ribosome recycling factor mutant R31A from M... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4kb4 | ||||||
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Title | Crystal structure of ribosome recycling factor mutant R31A from Mycobacterium tuberculosis | ||||||
![]() | Ribosome-recycling factor | ||||||
![]() | TRANSLATION / Ribosome recycling / post-termination complex / Elongation factor G / Bacterial cytosol | ||||||
Function / homology | ![]() translation termination factor activity / cytoplasmic translational termination / ribosomal large subunit binding / translational termination / peptidoglycan-based cell wall / translation / plasma membrane / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Selvaraj, M. / Govindan, A. / Seshadri, A. / Dubey, B. / Varshney, U. / Vijayan, M. | ||||||
![]() | ![]() Title: Molecular flexibility of Mycobacterium tuberculosis ribosome recycling factor and its functional consequences: an exploration involving mutants. Authors: Selvaraj, M. / Govindan, A. / Seshadri, A. / Dubey, B. / Varshney, U. / Vijayan, M. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 88.8 KB | Display | ![]() |
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PDB format | ![]() | 67.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 421.5 KB | Display | ![]() |
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Full document | ![]() | 426.2 KB | Display | |
Data in XML | ![]() | 10.4 KB | Display | |
Data in CIF | ![]() | 13.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4kawC ![]() 4kb2C ![]() 4kc6C ![]() 4kddC ![]() 1wqgS S: Starting model for refinement C: citing same article ( |
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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
#1: Protein | Mass: 20775.547 Da / Num. of mol.: 1 / Mutation: R31A Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() | ||
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#2: Chemical | #3: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.79 Å3/Da / Density % sol: 55.97 % |
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Crystal grow | Temperature: 298 K / Method: under oil in microbatch plates / pH: 7.8 Details: 6% Polyethylene glycol 4000, 20mM Tris-HCl, 0.6mM cadmium acetate, 5% polyethylene glycol 400, pH 7.8, Under oil in microbatch plates, temperature 298KK |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.514 Å / Relative weight: 1 |
Reflection | Resolution: 2.25→60.3 Å / Num. obs: 11114 / % possible obs: 100 % / Observed criterion σ(I): 2 / Redundancy: 4 % / Rmerge(I) obs: 0.087 |
Reflection shell | Resolution: 2.25→2.37 Å / Redundancy: 4 % / Rmerge(I) obs: 0.087 / Mean I/σ(I) obs: 12.5 / Num. unique all: 11114 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1WQG Resolution: 2.25→46.24 Å / Cor.coef. Fo:Fc: 0.934 / Cor.coef. Fo:Fc free: 0.924 / SU B: 11.282 / SU ML: 0.179 / Cross valid method: THROUGHOUT / ESU R: 0.286 / ESU R Free: 0.228 / 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: 1.2 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 50.503 Å2
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Refine analyze | Luzzati coordinate error free: 0.228 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.25→46.24 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.25→2.308 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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