1XMO

Crystal Structure of mnm5U34t6A37-tRNALysUUU Complexed with AAG-mRNA in the Decoding Center

Structural Biology Knowledgebase: 1XMO SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.25 Å
  • R-Value Free: 0.284
  • R-Value Work: 0.231

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 1XMO

Classification: RIBOSOME

Total Structure Weight: 791608.31


Macromolecule Entities
Molecule Chains Length Organism Details
30S ribosomal protein S2 B 256 Thermus thermophilus Gene Name(s): rpsB rps2 TTHA0861
30S ribosomal protein S3 C 239 Thermus thermophilus Gene Name(s): rpsC rps3 TTHA1686
30S ribosomal protein S4 D 209 Thermus thermophilus Gene Name(s): rpsD rps4 TTHA1665
30S ribosomal protein S5 E 162 Thermus thermophilus Gene Name(s): rpsE TTHA1675
30S ribosomal protein S6 F 101 Thermus thermophilus Gene Name(s): rpsF TTHA0245
30S ribosomal protein S7 G 156 Thermus thermophilus Gene Name(s): rpsG rps7 TTHA1696
30S ribosomal protein S8 H 138 Thermus thermophilus Gene Name(s): rpsH TTHA1678
30S ribosomal protein S9 I 128 Thermus thermophilus Gene Name(s): rpsI rps9 TTHA1464
30S ribosomal protein S10 J 105 Thermus thermophilus Gene Name(s): rpsJ TTHA1693
30S ribosomal protein S11 K 129 Thermus thermophilus Gene Name(s): rpsK rps11 TTHA1666
30S ribosomal protein S12 L 135 Thermus thermophilus Gene Name(s): rpsL TTHA1697
30S ribosomal protein S13 M 126 Thermus thermophilus Gene Name(s): rpsM rps13 TTHA1667
30S ribosomal protein S14 N 61 Thermus thermophilus Gene Name(s): rpsZ rpsN TTHA1679
30S ribosomal protein S15 O 89 Thermus thermophilus Gene Name(s): rpsO TTHA1138
30S ribosomal protein S16 P 88 Thermus thermophilus Gene Name(s): rpsP TTHA1035
30S ribosomal protein S17 Q 105 Thermus thermophilus Gene Name(s): rpsQ TTHA1683
30S ribosomal protein S18 R 88 Thermus thermophilus Gene Name(s): rpsR TTHA0243
30S ribosomal protein S19 S 93 Thermus thermophilus Gene Name(s): rpsS TTHA1688
30S ribosomal protein S20 T 106 Thermus thermophilus Gene Name(s): rpsT rps20 TTHA1397
30S ribosomal protein Thx V 27 Thermus thermophilus Gene Name(s): rpsU TTHA1396
Macromolecule Entities
Molecule Chains Length Organism Details
16S ribosomal RNA A 1522 Thermus thermophilus
A-Site Messenger RNA W 3 synthetic
Anticodon Transfer RNA X 11 synthetic

Small Molecules
Ligands 3 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
MG
Query on MG

A, J, X MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Ligand Explorer
 
JSmol
PAR
Query on PAR

A PAROMOMYCIN
PAROMOMYCIN I, AMMINOSIDIN, CATENULIN, CRESTOMYCIN, MONOMYCIN A, NEOMYCIN E (Synonym)
C23 H45 N5 O14
UOZODPSAJZTQNH-LSWIJEOBSA-N
Ligand Explorer
 
JSmol
ZN
Query on ZN

D, N ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
Ligand Explorer
 
JSmol
Modified Residues 2 Unique
ID Chains Type Formula 2D Diagram Parent
MNU
Query on MNU
X RNA LINKING C11 H18 N3 O9 P U
T6A
Query on T6A
X RNA LINKING C15 H21 N6 O11 P A

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.25 Å
  • R-Value Free: 0.284
  • R-Value Work: 0.231
  • Space Group: P 41 21 2
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 400.81 α = 90.00
b = 400.81 β = 90.00
c = 176.13 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2004-10-04
  • Released Date: 2004-12-14
  • Deposition author(s): Murphy, F.V., Ramakrishnan, V., Malkiewicz, A., Agris, P.F.

Revision History

  • 2011-07-13
    Type: Version format compliance | Details: compliance with PDB Exchange Dictionary V4
  • 2011-07-13
    Type: Source and taxonomy | Details: Removed strain from scientific name