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- PDB-4kdd: Structure of Mycobacterium tuberculosis ribosome recycling factor... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4kdd | ||||||
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Title | Structure of Mycobacterium tuberculosis ribosome recycling factor in presence of detergent | ||||||
![]() | Ribosome-recycling factor | ||||||
![]() | TRANSLATION / eubacteria / 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 | ![]() | 90.1 KB | Display | ![]() |
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PDB format | ![]() | 67.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 721.5 KB | Display | ![]() |
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Full document | ![]() | 727.5 KB | Display | |
Data in XML | ![]() | 12.6 KB | Display | |
Data in CIF | ![]() | 17.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4kawC ![]() 4kb2C ![]() 4kb4C ![]() 4kc6C ![]() 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: 20861.664 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() | ||||
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#2: Chemical | #3: Sugar | ChemComp-DMU / | #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.58 Å3/Da / Density % sol: 52.37 % |
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Crystal grow | Temperature: 298 K / Method: under oil in microbatch plates / pH: 7.8 Details: 6% polyethylene glycol 4000, 100mM Tris HCl, 0.6mM Cadmium acetate, 5% polyethylene glycol 400, pH 7.8, Under oil in microbatch plates, temperature 298K |
-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 29, 2009 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.514 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→33.74 Å / Num. all: 17141 / Num. obs: 17141 / % possible obs: 99.9 % / Observed criterion σ(I): 2 / Redundancy: 3.9 % / Rmerge(I) obs: 0.133 |
Reflection shell | Resolution: 1.9→2 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.133 / Mean I/σ(I) obs: 7.2 / Num. unique all: 17141 / % possible all: 99.9 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1WQG Resolution: 1.9→33.7 Å / Cor.coef. Fo:Fc: 0.896 / Cor.coef. Fo:Fc free: 0.894 / SU B: 7.44 / SU ML: 0.138 / Cross valid method: THROUGHOUT / ESU R: 0.199 / ESU R Free: 0.167 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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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: BABINET MODEL WITH MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 26.495 Å2
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Refine analyze | Luzzati coordinate error free: 0.167 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.9→33.7 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.9→1.949 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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