5XYM Ribosome date Jul 09, 2017
title Large Subunit Of Mycobacterium Smegmatis
authors Z.Li, X.Ge, Y.Zhang, L.Zheng, S.Sanyal, N.Gao
compound source
Molecule: 50s Ribosomal Protein L32
Chain
Synonym: Bl32
Organism_scientific: Mycobacterium Smegmatis (Strain Atcc 7 Mc(2)155);
Organism_taxid: 246196
Strain: Atcc 700084 Mc(2)155

Molecule: 50s Ribosomal Protein L33 2
Chain: 1
Synonym: Bl33

Organism_scientific: Mycobacterium Smegmatis (Strain Atcc 7 Mc(2)155);
Organism_taxid: 246196
Strain: Atcc 700084 Mc(2)155

Molecule: 50s Ribosomal Protein L34
Chain: 2
Synonym: Bl34

Organism_scientific: Mycobacterium Smegmatis (Strain Atcc 7 Mc(2)155);
Organism_taxid: 246196
Strain: Atcc 700084 Mc(2)155

Molecule: 50s Ribosomal Protein L35
Chain: 3
Synonym: Bl35

Organism_scientific: Mycobacterium Smegmatis (Strain Atcc 7 Mc(2)155);
Organism_taxid: 246196
Strain: Atcc 700084 Mc(2)155

Molecule: 50s Ribosomal Protein L36
Chain: 4
Synonym: Bl36

Organism_scientific: Mycobacterium Smegmatis (Strain Atcc 7 Mc(2)155);
Organism_taxid: 246196
Strain: Atcc 700084 Mc(2)155

Molecule: 23s Rna
Chain: A

Organism_scientific: Mycobacterium Smegmatis (Strain Atcc 7 Mc(2)155);
Organism_taxid: 246196
Strain: Atcc 700084 Mc(2)155

Molecule: 5s Rna
Chain: B

Organism_scientific: Mycobacterium Smegmatis (Strain Atcc 7 Mc(2)155);
Organism_taxid: 246196
Strain: Atcc 700084 Mc(2)155

Molecule: 50s Ribosomal Protein L2
Chain: C
Synonym: Ul2

Organism_scientific: Mycobacterium Smegmatis (Strain Atcc 7 Mc(2)155);
Organism_taxid: 246196
Strain: Atcc 700084 Mc(2)155

Molecule: 50s Ribosomal Protein L3
Chain: D
Synonym: Ul3

Organism_scientific: Mycobacterium Smegmatis (Strain Atcc 7 Mc(2)155);
Organism_taxid: 246196
Strain: Atcc 700084 Mc(2)155

Molecule: 50s Ribosomal Protein L4
Chain: E
Synonym: Ul4

Organism_scientific: Mycobacterium Smegmatis (Strain Atcc 7 Mc(2)155);
Organism_taxid: 246196
Strain: Atcc 700084 Mc(2)155

Molecule: 50s Ribosomal Protein L5
Chain: F
Synonym: Ul5

Organism_scientific: Mycobacterium Smegmatis (Strain Atcc 7 Mc(2)155);
Organism_taxid: 246196
Strain: Atcc 700084 Mc(2)155

Molecule: 50s Ribosomal Protein L6
Chain: G
Synonym: Ul6

Organism_scientific: Mycobacterium Smegmatis (Strain Atcc 7 Mc(2)155);
Organism_taxid: 246196
Strain: Atcc 700084 Mc(2)155

Molecule: 50s Ribosomal Protein L9
Chain: H
Synonym: Bl9

Organism_scientific: Mycobacterium Smegmatis (Strain Atcc 7 Mc(2)155);
Organism_taxid: 246196
Strain: Atcc 700084 Mc(2)155

Molecule: 50s Ribosomal Protein L13
Chain: J
Synonym: Ul13

Organism_scientific: Mycobacterium Smegmatis (Strain Atcc 7 Mc(2)155);
Organism_taxid: 246196
Strain: Atcc 700084 Mc(2)155

Molecule: 50s Ribosomal Protein L14
Chain: K
Synonym: Ul14

Organism_scientific: Mycobacterium Smegmatis (Strain Atcc 7 Mc(2)155);
Organism_taxid: 246196
Strain: Atcc 700084 Mc(2)155

Molecule: 50s Ribosomal Protein L15
Chain: L
Synonym: Ul15

Organism_scientific: Mycobacterium Smegmatis (Strain Atcc 7 Mc(2)155);
Organism_taxid: 246196
Strain: Atcc 700084 Mc(2)155

Molecule: 50s Ribosomal Protein L16
Chain: M
Synonym: Ul16

Organism_scientific: Mycobacterium Smegmatis (Strain Atcc 7 Mc(2)155);
Organism_taxid: 246196
Strain: Atcc 700084 Mc(2)155

Molecule: 50s Ribosomal Protein L17
Chain: N
Synonym: Bl17

Organism_scientific: Mycobacterium Smegmatis (Strain Atcc 7 Mc(2)155);
Organism_taxid: 246196
Strain: Atcc 700084 Mc(2)155

Molecule: 50s Ribosomal Protein L18
Chain: O
Synonym: Ul18

Organism_scientific: Mycobacterium Smegmatis (Strain Atcc 7 Mc(2)155);
Organism_taxid: 246196
Strain: Atcc 700084 Mc(2)155

Molecule: 50s Ribosomal Protein L19
Chain: P
Synonym: Bl19

Organism_scientific: Mycobacterium Smegmatis (Strain Atcc 7 Mc(2)155);
Organism_taxid: 246196
Strain: Atcc 700084 Mc(2)155

Molecule: 50s Ribosomal Protein L20
Chain: Q
Synonym: Bl20

Organism_scientific: Mycobacterium Smegmatis (Strain Atcc 7 Mc(2)155);
Organism_taxid: 246196
Strain: Atcc 700084 Mc(2)155

Molecule: 50s Ribosomal Protein L21
Chain: R
Synonym: Bl21

Organism_scientific: Mycobacterium Smegmatis (Strain Atcc 7 Mc(2)155);
Organism_taxid: 246196
Strain: Atcc 700084 Mc(2)155

Molecule: 50s Ribosomal Protein L22
Chain: S
Synonym: Ul22

Organism_scientific: Mycobacterium Smegmatis (Strain Atcc 7 Mc(2)155);
Organism_taxid: 246196
Strain: Atcc 700084 Mc(2)155

Molecule: 50s Ribosomal Protein L23
Chain: T
Synonym: Ul23

Organism_scientific: Mycobacterium Smegmatis (Strain Atcc 7 Mc(2)155);
Organism_taxid: 246196
Strain: Atcc 700084 Mc(2)155

Molecule: 50s Ribosomal Protein L24
Chain: U
Synonym: Ul24

Organism_scientific: Mycobacterium Smegmatis (Strain Atcc 7 Mc(2)155);
Organism_taxid: 246196
Strain: Atcc 700084 Mc(2)155

Molecule: 50s Ribosomal Protein L25
Chain: V
Synonym: Bl25

Organism_scientific: Mycobacterium Smegmatis (Strain Atcc 7 Mc(2)155);
Organism_taxid: 246196
Strain: Atcc 700084 Mc(2)155

Molecule: 50s Ribosomal Protein L27
Chain: W
Synonym: Bl27

Organism_scientific: Mycobacterium Smegmatis (Strain Atcc 7 Mc(2)155);
Organism_taxid: 246196
Strain: Atcc 700084 Mc(2)155

Molecule: 50s Ribosomal Protein L28
Chain: X
Synonym: Bl28

Organism_scientific: Mycobacterium Smegmatis (Strain Atcc 7 Mc(2)155);
Organism_taxid: 246196
Strain: Atcc 700084 Mc(2)155

Molecule: 50s Ribosomal Protein L29
Chain: Y
Synonym: Ul29

Organism_scientific: Mycobacterium Smegmatis (Strain Atcc 7 Mc(2)155);
Organism_taxid: 246196
Strain: Atcc 700084 Mc(2)155

Molecule: 50s Ribosomal Protein L30
Chain: Z
Synonym: Ul30

Organism_scientific: Mycobacterium Smegmatis (Strain Atcc 7 Mc(2)155);
Organism_taxid: 246196
Strain: Atcc 700084 Mc(2)155

Molecule: Uncharacterized Protein Bl37
Chain: a

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 3.08 Å
Gene
Ontology
ChainFunctionProcessComponent
0


1


2


3


4


C


D


E


F


G


H


J


K


L


M


N


O


P


Q


R


S


T


U


V


W


X


Y


Z


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] (1665 Kb) [Save to disk]
  • Biological Unit Coordinates (5xym.pdb1.gz) 1649 Kb
  • CSU: Contacts of Structural Units for 5XYM
  • Retrieve 5XYM in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 5XYM from S2C, [Save to disk]
  • View 5XYM 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 5XYM
  • Cartoon representation from PDB Cartoon
  • Ramachandran plot from PDBSum
  • Structure-derived information
  • Dipole moment, from Dipole Server at Weizmann Institute
  • Crystal Contacts, from CryCo at Weizmann Institute
  • Fold representative 5xym from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [5xym_O] [5xym_R] [5xym_M] [5xym_L] [5xym_G] [5xym_S] [5xym_A] [5xym_Q] [5xym_H] [5xym_a] [5xym_K] [5xym_U] [5xym_3] [5xym_B] [5xym_Y] [5xym_0] [5xym_T] [5xym_V] [5xym_2] [5xym_J] [5xym_X] [5xym_F] [5xym_W] [5xym_4] [5xym_1] [5xym_N] [5xym_E] [5xym_Z] [5xym_P] [5xym_C] [5xym_D]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Other resources with information on 5XYM
  • Community annotation for 5XYM at PDBWiki (http://pdbwiki.org)

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