1N33

Structure of the Thermus thermophilus 30S ribosomal subunit bound to codon and near-cognate transfer rna anticodon stem-loop mismatched at the second codon position at the a site with paromomycin

Structural Biology Knowledgebase: 1N33 SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.35 Å
  • R-Value Free: 0.284
  • R-Value Work: 0.225

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 1N33

Classification: RIBOSOME

Total Structure Weight: 793101.68


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 208 Thermus thermophilus Gene Name(s): rpsD rps4 TTHA1665
30S RIBOSOMAL PROTEIN S5 E 161 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 155 Thermus thermophilus Gene Name(s): rpsG rps7 TTHA1696
30S RIBOSOMAL PROTEIN S8 H 138 Thermus thermophilus Mutation: E25D, K37R, E52D, I61V, H62Y, K81H, R88K, P115S
Gene Name(s): rpsH TTHA1678
30S RIBOSOMAL PROTEIN S9 I 128 Thermus thermophilus Gene Name(s): rpsI rps9 TTHA1464
30S RIBOSOMAL PROTEIN S10 J 104 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 60 Thermus thermophilus Gene Name(s): rpsZ rpsN TTHA1679
30S RIBOSOMAL PROTEIN S15 O 88 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 104 Thermus thermophilus Mutation: R50K, V53L, A62S, E79S, L82M, V90I, A96Q
Gene Name(s): rpsQ TTHA1683
30S RIBOSOMAL PROTEIN S18 R 88 Thermus thermophilus Gene Name(s): rpsR TTHA0243
30S RIBOSOMAL PROTEIN S19 S 92 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 26 Thermus thermophilus EC#: 4.1.1.3 IUBMB
Gene Name(s): rpsU TTHA1396
Macromolecule Entities
Molecule Chains Length Organism Details
16S RIBOSOMAL RNA A 1522 Thermus thermophilus
ANTICODON STEM-LOOP OF SER TRANSFER RNA Y 17 Thermus thermophilus
A-SITE MESSENGER RNA FRAGMENT Z 6 Thermus thermophilus

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

A PAROMOMYCIN
CATENULIN,, AMMINOSIDIN (Synonym)
C23 H45 N5 O14
UOZODPSAJZTQNH-LSWIJEOBSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
ZN
Query on ZN

D, N ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
MG
Query on MG

A, Y, Z MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
Modified Residues 1 Unique
ID Chains Type Formula 2D Diagram Parent
PSU
Query on PSU
Y RNA LINKING C9 H13 N2 O9 P U

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.35 Å
  • R-Value Free: 0.284
  • R-Value Work: 0.225
  • Space Group: P 41 21 2
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 401.60 α = 90.00
b = 401.60 β = 90.00
c = 176.02 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2002-10-25
  • Released Date: 2002-11-29
  • Deposition author(s): Ogle, J.M., Murphy IV, F.V., Tarry, M.J., Ramakrishnan, V.

Revision History

  • 2011-07-13
    Type: Version format compliance | Details: compliance with PDB Exchange Dictionary V4