+Open data
-Basic information
Entry | Database: PDB / ID: 6jmk | ||||||
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Title | Ribosomal protein S7 from Mycobacterium tuberculosis | ||||||
Components | 30S ribosomal protein S7 | ||||||
Keywords | RIBOSOMAL PROTEIN / S7 / Mycobacterium tuberculosis | ||||||
Function / homology | Function and homology information peptidoglycan-based cell wall / ribosomal small subunit assembly / cytosolic small ribosomal subunit / tRNA binding / rRNA binding / ribosome / structural constituent of ribosome / translation / mRNA binding / plasma membrane / cytosol Similarity search - Function | ||||||
Biological species | Mycobacterium tuberculosis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å | ||||||
Authors | Li, Z. / Li, J. | ||||||
Funding support | China, 1items
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Citation | Journal: Biochem. Biophys. Res. Commun. / Year: 2019 Title: Structural insights into the complex of trigger factor chaperone and ribosomal protein S7 from Mycobacterium tuberculosis. Authors: Li, Z. / Wu, D. / Zhan, B. / Hu, X. / Gan, J. / Ji, C. / Li, J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6jmk.cif.gz | 75.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6jmk.ent.gz | 53.8 KB | Display | PDB format |
PDBx/mmJSON format | 6jmk.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/jm/6jmk ftp://data.pdbj.org/pub/pdb/validation_reports/jm/6jmk | HTTPS FTP |
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-Related structure data
Related structure data | 1husS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 17720.496 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv) (bacteria) Strain: ATCC 25618 / H37Rv / Gene: rpsG, rps7, Rv0683, MTV040.11 Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria) References: UniProt: P9WH29 #2: Chemical | #3: Chemical | ChemComp-EDO / | #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.84 Å3/Da / Density % sol: 56.72 % |
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Crystal grow | Temperature: 291.15 K / Method: vapor diffusion, hanging drop / Details: 0.2M potassium tartrate, 20% PEG 3350 |
-Data collection
Diffraction | Mean temperature: 80 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97928 Å |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Oct 19, 2017 |
Radiation | Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97928 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→41.31 Å / Num. obs: 38244 / % possible obs: 99.95 % / Redundancy: 2 % / CC1/2: 0.996 / Rmerge(I) obs: 0.033 / Rrim(I) all: 0.047 / Net I/σ(I): 11.88 |
Reflection shell | Resolution: 1.8→1.864 Å / Rmerge(I) obs: 0.1508 / Mean I/σ(I) obs: 4.09 / Num. unique obs: 3755 / CC1/2: 0.885 / Rrim(I) all: 0.2133 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1HUS Resolution: 1.8→41.31 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.943 / SU B: 2.165 / SU ML: 0.068 / Cross valid method: THROUGHOUT / ESU R: 0.102 / ESU R Free: 0.101 / 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 25.337 Å2
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Refinement step | Cycle: 1 / Resolution: 1.8→41.31 Å
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Refine LS restraints |
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