1XMO Ribosome date Oct 04, 2004
title Crystal Structure Of Mnm5u34t6a37-Trnalysuuu Complexed With In The Decoding Center
authors F.V.Murphy, V.Ramakrishnan, A.Malkiewicz, P.F.Agris
compound source
Molecule: 16s Ribosomal Rna
Chain: A
 Organism_scientific: Thermus Thermophilus
Organism_taxid: 262724
Strain: Hb27

Molecule: A-Site Messenger Rna
Chain: W
Engineered: Yes
Synthetic: Yes

Molecule: Anticodon Transfer Rna
Chain: X
Engineered: Yes
Synthetic: Yes

Molecule: 30s Ribosomal Protein S2
Chain: B
Organism_scientific: Thermus Thermophilus
Organism_taxid: 274

Molecule: 30s Ribosomal Protein S3
Chain: C
Organism_scientific: Thermus Thermophilus
Organism_taxid: 274

Molecule: 30s Ribosomal Protein S4
Chain: D
Organism_scientific: Thermus Thermophilus
Organism_taxid: 274

Molecule: 30s Ribosomal Protein S5
Chain: E
Organism_scientific: Thermus Thermophilus
Organism_taxid: 274

Molecule: 30s Ribosomal Protein S6
Chain: F
Synonym: Ts9
Organism_scientific: Thermus Thermophilus
Organism_taxid: 274

Molecule: 30s Ribosomal Protein S7
Chain: G
Organism_scientific: Thermus Thermophilus
Organism_taxid: 274

Molecule: 30s Ribosomal Protein S8
Chain: H
Organism_scientific: Thermus Thermophilus
Organism_taxid: 274

Molecule: 30s Ribosomal Protein S9
Chain: I
Organism_scientific: Thermus Thermophilus
Organism_taxid: 274

Molecule: 30s Ribosomal Protein S10
Chain: J
Organism_scientific: Thermus Thermophilus
Organism_taxid: 274

Molecule: 30s Ribosomal Protein S11
Chain: K
Organism_scientific: Thermus Thermophilus
Organism_taxid: 274

Molecule: 30s Ribosomal Protein S12
Chain: L
Organism_scientific: Thermus Thermophilus
Organism_taxid: 274

Molecule: 30s Ribosomal Protein S13
Chain: M
Organism_scientific: Thermus Thermophilus
Organism_taxid: 274

Molecule: 30s Ribosomal Protein S14
Chain: N
Organism_scientific: Thermus Thermophilus
Organism_taxid: 274

Molecule: 30s Ribosomal Protein S15
Chain: O
Organism_scientific: Thermus Thermophilus
Organism_taxid: 274

Molecule: 30s Ribosomal Protein S16
Chain: P
Organism_scientific: Thermus Thermophilus
Organism_taxid: 274

Molecule: 30s Ribosomal Protein S17
Chain: Q
Organism_scientific: Thermus Thermophilus
Organism_taxid: 274

Molecule: 30s Ribosomal Protein S18
Chain: R
Organism_scientific: Thermus Thermophilus
Organism_taxid: 274

Molecule: 30s Ribosomal Protein S19
Chain: S
Organism_scientific: Thermus Thermophilus
Organism_taxid: 274

Molecule: 30s Ribosomal Protein S20
Chain: T
Organism_scientific: Thermus Thermophilus
Organism_taxid: 274

Molecule: 30s Ribosomal Protein Thx
Chain: V
Organism_scientific: Thermus Thermophilus
Organism_taxid: 274
symmetry Space Group: P 41 21 2
R_factor 0.231 R_Free 0.284
crystal
cell
length a length b length c angle alpha angle beta angle gamma
400.811 400.811 176.125 90.00 90.00 90.00
method X-Ray Diffractionresolution 3.25 Å
ligand MG, MNU, PAR, T6A, ZN enzyme
Gene
Ontology
ChainFunctionProcessComponent
B


C


D


E


F


G


H


I


J


K


L


M


N


O


P


Q


R


S


T


V


Primary referenceThe role of modifications in codon discrimination by tRNA(Lys)UUU., Murphy FV 4th, Ramakrishnan V, Malkiewicz A, Agris PF, Nat Struct Mol Biol 2004 Dec;11(12):1186-91. Epub . PMID:15558052
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (938 Kb) [Save to disk]
  • Biological Unit Coordinates (1xmo.pdb1.gz) 926 Kb
  • LPC: Ligand-Protein Contacts for 1XMO
  • CSU: Contacts of Structural Units for 1XMO
  • Likely Quarternary Molecular Structure file(s) for 1XMO
  • Structure Factors (2786 Kb)
  • Retrieve 1XMO in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 1XMO from S2C, [Save to disk]
  • Re-refined 1xmo structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
    • View 1XMO 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 1XMO
  • Ramachandran plot from PDBSum
    • Structure-derived information
  • Electron Density related parameters from EDS Electron Density Server, at Upsala
  • Dipole moment, from Dipole Server at Weizmann Institute
  • 3D motif for 1XMO, from MSDmotif at EBI
  • Classification of representative domains in scop (Structural Classification of Proteins)
        - Domain d1xmob_, region B [Jmol] [rasmolscript] [script source]
        - Domain d1xmoc2, region C:107-207 [Jmol] [rasmolscript] [script source]
        - Domain d1xmoc1, region C:2-106 [Jmol] [rasmolscript] [script source]
        - Domain d1xmod_, region D [Jmol] [rasmolscript] [script source]
        - Domain d1xmoe2, region E:5-73 [Jmol] [rasmolscript] [script source]
        - Domain d1xmoe1, region E:74-154 [Jmol] [rasmolscript] [script source]
        - Domain d1xmof_, region F [Jmol] [rasmolscript] [script source]
        - Domain d1xmog_, region G [Jmol] [rasmolscript] [script source]
        - Domain d1xmoh_, region H [Jmol] [rasmolscript] [script source]
        - Domain d1xmoi_, region I [Jmol] [rasmolscript] [script source]
        - Domain d1xmoj_, region J [Jmol] [rasmolscript] [script source]
        - Domain d1xmok_, region K [Jmol] [rasmolscript] [script source]
        - Domain d1xmol_, region L [Jmol] [rasmolscript] [script source]
        - Domain d1xmom_, region M [Jmol] [rasmolscript] [script source]
        - Domain d1xmon_, region N [Jmol] [rasmolscript] [script source]
        - Domain d1xmoo_, region O [Jmol] [rasmolscript] [script source]
        - Domain d1xmop_, region P [Jmol] [rasmolscript] [script source]
        - Domain d1xmoq_, region Q [Jmol] [rasmolscript] [script source]
        - Domain d1xmor_, region R [Jmol] [rasmolscript] [script source]
        - Domain d1xmos_, region S [Jmol] [rasmolscript] [script source]
        - Domain d1xmot_, region T [Jmol] [rasmolscript] [script source]
        - Domain d1xmov_, region V [Jmol] [rasmolscript] [script source]
    • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [1xmo_B] [1xmo_L] [1xmo_T] [1xmo_S] [1xmo_K] [1xmo_G] [1xmo_O] [1xmo_H] [1xmo_A] [1xmo_I] [1xmo_P] [1xmo_J] [1xmo_C] [1xmo_W] [1xmo_X] [1xmo_R] [1xmo_N] [1xmo_D] [1xmo_Q] [1xmo_F] [1xmo_E] [1xmo_V] [1xmo_M] [1xmo]
  • SWISS-PROT database: [Q5SHN7] [P80376] [Q5SHN3] [P80377] [Q5SHQ1] [Q5SJ76] [Q5SJH3] [Q5SHP7] [Q5SLQ0] [Q5SHP2] [P80380] [P80371] [P80372] [P80373] [Q5SHQ5] [Q5SLP8] [P17291] [Q5SHQ2] [P80374] [Q5SIH3]
  • Domain organization of [RS10_THET8] [RS11_THET8] [RS12_THET8] [RS13_THET8] [RS14Z_THET8] [RS15_THET8] [RS16_THET8] [RS17_THET8] [RS18_THET8] [RS19_THET8] [RS20_THET8] [RS2_THET8] [RS3_THET8] [RS4_THET8] [RS5_THET8] [RS6_THET8] [RS7_THET8] [RS8_THET8] [RS9_THET8] [RSHX_THET8] by SWISSPFAM
  • Domains found in 1XMO: [KH] [Ribosomal_S10] [Ribosomal_S15] [Ribosomal_S4] [S4 ] by SMART
    • Other resources with information on 1XMO
  • Community annotation for 1XMO at PDBWiki (http://pdbwiki.org)
  • MMDB (Entrez's Structure Database)
    • Movements, Movies and Images
  • Images from IMB Jena Image Library of Biological Macromolecules.

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