+Open data
-Basic information
Entry | Database: PDB / ID: 5xym | ||||||
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Title | Large subunit of Mycobacterium smegmatis | ||||||
Components |
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Keywords | RIBOSOME / Mycobacterium smegmatis ribosome / rRNA / rprotein | ||||||
Function / homology | Function and homology information large ribosomal subunit / ribosomal large subunit assembly / transferase activity / 5S rRNA binding / cytosolic large ribosomal subunit / tRNA binding / rRNA binding / ribosome / structural constituent of ribosome / ribonucleoprotein complex ...large ribosomal subunit / ribosomal large subunit assembly / transferase activity / 5S rRNA binding / cytosolic large ribosomal subunit / tRNA binding / rRNA binding / ribosome / structural constituent of ribosome / ribonucleoprotein complex / translation / cytoplasm Similarity search - Function | ||||||
Biological species | Mycobacterium smegmatis (bacteria) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.08 Å | ||||||
Authors | Li, Z. / Ge, X. / Zhang, Y. / Zheng, L. / Sanyal, S. / Gao, N. | ||||||
Citation | Journal: Protein Cell / Year: 2018 Title: Cryo-EM structure of Mycobacterium smegmatis ribosome reveals two unidentified ribosomal proteins close to the functional centers. Authors: Zhifei Li / Xueliang Ge / Yixiao Zhang / Lvqin Zheng / Suparna Sanyal / Ning Gao / | ||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 5xym.cif.gz | 2.1 MB | Display | PDBx/mmCIF format |
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PDB format | pdb5xym.ent.gz | 1.6 MB | Display | PDB format |
PDBx/mmJSON format | 5xym.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5xym_validation.pdf.gz | 1 MB | Display | wwPDB validaton report |
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Full document | 5xym_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 5xym_validation.xml.gz | 128.4 KB | Display | |
Data in CIF | 5xym_validation.cif.gz | 216.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xy/5xym ftp://data.pdbj.org/pub/pdb/validation_reports/xy/5xym | HTTPS FTP |
-Related structure data
Related structure data | 6789MC 6790C 5xyuC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
+50S ribosomal protein ... , 28 types, 28 molecules 01234CDEFGHJKLMNOPQRSTUVWXYZ
-RNA chain , 2 types, 2 molecules AB
#6: RNA chain | Mass: 1026283.438 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155) (bacteria) Strain: ATCC 700084 / mc(2)155 |
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#7: RNA chain | Mass: 38038.777 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155) (bacteria) Strain: ATCC 700084 / mc(2)155 / References: GenBank: 118168627 |
-Protein/peptide / Non-polymers , 2 types, 147 molecules a
#31: Protein/peptide | Mass: 2841.375 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155) (bacteria) Strain: ATCC 700084 / mc(2)155 / References: UniProt: A0QTP4 |
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#32: Chemical | ChemComp-MG / |
-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: Large subunit of Mycobacterium smegmatis ribosome / Type: RIBOSOME / Entity ID: #1-#31 / Source: NATURAL |
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Source (natural) | Organism: Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155) (bacteria) Strain: ATCC 700084 / mc(2)155 |
Buffer solution | pH: 7.6 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Cryogen name: ETHANE |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD |
Image recording | Electron dose: 2 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k) |
-Processing
CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION |
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3D reconstruction | Resolution: 3.08 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 71351 / Symmetry type: POINT |