5XYU Ribosome date Jul 10, 2017
title Small Subunit Of Mycobacterium Smegmatis Ribosome
authors Z.Li, Y.Zhang, L.Zheng, X.Ge, S.Sanyal, N.Gao
compound source
Molecule: 16s Rna
Chain: A
 Organism_scientific: Mycobacterium Smegmatis (Strain Atcc 7 Mc(2)155);
Organism_taxid: 246196
Strain: Atcc 700084 Mc(2)155

Molecule: 30s Ribosomal Protein S3
Chain: C
Synonym: Us3
Organism_scientific: Mycobacterium Smegmatis (Strain Atcc 7 Mc(2)155);
Organism_taxid: 246196
Strain: Atcc 700084 Mc(2)155

Molecule: 30s Ribosomal Protein S4
Chain: D
Synonym: Us4
Organism_scientific: Mycobacterium Smegmatis (Strain Atcc 7 Mc(2)155);
Organism_taxid: 246196
Strain: Atcc 700084 Mc(2)155

Molecule: 30s Ribosomal Protein S5
Chain: E
Synonym: Us5
Organism_scientific: Mycobacterium Smegmatis (Strain Atcc 7 Mc(2)155);
Organism_taxid: 246196
Strain: Atcc 700084 Mc(2)155

Molecule: 30s Ribosomal Protein S6
Chain: F
Synonym: Bs6
Organism_scientific: Mycobacterium Smegmatis (Strain Atcc 7 Mc(2)155);
Organism_taxid: 246196
Strain: Atcc 700084 Mc(2)155

Molecule: 30s Ribosomal Protein S7
Chain: G
Synonym: Us7
Organism_scientific: Mycobacterium Smegmatis (Strain Atcc 7 Mc(2)155);
Organism_taxid: 246196
Strain: Atcc 700084 Mc(2)155

Molecule: 30s Ribosomal Protein S8
Chain: H
Synonym: Us8
Organism_scientific: Mycobacterium Smegmatis (Strain Atcc 7 Mc(2)155);
Organism_taxid: 246196
Strain: Atcc 700084 Mc(2)155

Molecule: 30s Ribosomal Protein S9
Chain: I
Synonym: Us9
Organism_scientific: Mycobacterium Smegmatis (Strain Atcc 7 Mc(2)155);
Organism_taxid: 246196
Strain: Atcc 700084 Mc(2)155

Molecule: 30s Ribosomal Protein S10
Chain: J
Synonym: Us10
Organism_scientific: Mycobacterium Smegmatis (Strain Atcc 7 Mc(2)155);
Organism_taxid: 246196
Strain: Atcc 700084 Mc(2)155

Molecule: 30s Ribosomal Protein S11
Chain: K
Synonym: Us11
Organism_scientific: Mycobacterium Smegmatis (Strain Atcc 7 Mc(2)155);
Organism_taxid: 246196
Strain: Atcc 700084 Mc(2)155

Molecule: 30s Ribosomal Protein S12
Chain: L
Synonym: Us12
Organism_scientific: Mycobacterium Smegmatis (Strain Atcc 7 Mc(2)155);
Organism_taxid: 246196
Strain: Atcc 700084 Mc(2)155

Molecule: 30s Ribosomal Protein S13
Chain: M
Synonym: Us13
Organism_scientific: Mycobacterium Smegmatis (Strain Atcc 7 Mc(2)155);
Organism_taxid: 246196
Strain: Atcc 700084 Mc(2)155

Molecule: 30s Ribosomal Protein S14 Type Z
Chain: N
Synonym: Us14
Organism_scientific: Mycobacterium Smegmatis (Strain Atcc 7 Mc(2)155);
Organism_taxid: 246196
Strain: Atcc 700084 Mc(2)155

Molecule: 30s Ribosomal Protein S15
Chain: O
Synonym: Us15
Organism_scientific: Mycobacterium Smegmatis (Strain Atcc 7 Mc(2)155);
Organism_taxid: 246196
Strain: Atcc 700084 Mc(2)155

Molecule: 30s Ribosomal Protein S16
Chain: P
Synonym: Bs16
Organism_scientific: Mycobacterium Smegmatis (Strain Atcc 7 Mc(2)155);
Organism_taxid: 246196
Strain: Atcc 700084 Mc(2)155

Molecule: 30s Ribosomal Protein S17
Chain: Q
Synonym: Us17
Organism_scientific: Mycobacterium Smegmatis (Strain Atcc 7 Mc(2)155);
Organism_taxid: 246196
Strain: Atcc 700084 Mc(2)155

Molecule: 30s Ribosomal Protein S18 2
Chain: R
Synonym: Bs18
Organism_scientific: Mycobacterium Smegmatis (Strain Atcc 7 Mc(2)155);
Organism_taxid: 246196
Strain: Atcc 700084 Mc(2)155

Molecule: 30s Ribosomal Protein S19
Chain: S
Synonym: Us19
Organism_scientific: Mycobacterium Smegmatis (Strain Atcc 7 Mc(2)155);
Organism_taxid: 246196
Strain: Atcc 700084 Mc(2)155

Molecule: 30s Ribosomal Protein S20
Chain: T
Synonym: Bs20
Organism_scientific: Mycobacterium Smegmatis (Strain Atcc 7 Mc(2)155);
Organism_taxid: 246196
Strain: Atcc 700084 Mc(2)155

Molecule: Conserved Domain Protein
Chain: U
Synonym: Ul41
Organism_scientific: Mycobacterium Smegmatis (Strain Atcc 7 Mc(2)155);
Organism_taxid: 246196
Strain: Atcc 700084 Mc(2)155
symmetry Space Group: P 1
R_factor
R_Free
crystal
cell
length a length b length c angle alpha angle beta angle gamma
1.000 1.000 1.000 90.00 90.00 90.00
method Electron Microscopyresolution 3.45 Å
ligand MG enzyme
Gene
Ontology
ChainFunctionProcessComponent
C


D


E


F


G


H


I


J


K


L


M


N


O


P


Q


R


S


T


Primary referenceCryo-EM structure of Mycobacterium smegmatis ribosome reveals two unidentified ribosomal proteins close to the functional centers., Li Z, Ge X, Zhang Y, Zheng L, Sanyal S, Gao N, Protein Cell. 2017 Sep 5. doi: 10.1007/s13238-017-0456-9. PMID:28875450
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (894 Kb) [Save to disk]
  • Biological Unit Coordinates (5xyu.pdb1.gz) 886 Kb
  • LPC: Ligand-Protein Contacts for 5XYU
  • CSU: Contacts of Structural Units for 5XYU
  • Retrieve 5XYU in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 5XYU from S2C, [Save to disk]
    • View 5XYU in 3D
  • Proteopedia, because life has more than 2D.
  • On Jmol, a nice Rasmol like molecule viewer. This is good for easiest viewing of basic structure.
  • On FirstGlance, an excellent tool for a guided tour on the structure components, by E. Martz.
    • Visual 3D analysis of 5XYU
  • Ramachandran plot from PDBSum
    • Structure-derived information
  • Dipole moment, from Dipole Server at Weizmann Institute
    • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [5xyu_A] [5xyu_N] [5xyu_J] [5xyu_I] [5xyu_T] [5xyu_K] [5xyu_R] [5xyu_P] [5xyu_O] [5xyu_E] [5xyu_M] [5xyu_S] [5xyu_H] [5xyu_U] [5xyu_D] [5xyu_L] [5xyu_G] [5xyu_F] [5xyu_Q] [5xyu_C]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
    • Other resources with information on 5XYU
  • Community annotation for 5XYU at PDBWiki (http://pdbwiki.org)

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