2UXD

Crystal structure of an extended tRNA anticodon stem loop in complex with its cognate mRNA CGGG in the context of the Thermus thermophilus 30S subunit.

Structural Biology Knowledgebase: 2UXD SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.2 Å
  • R-Value Free: 0.282
  • R-Value Work: 0.238

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 2UXD

Classification: RIBOSOME

Total Structure Weight: 793795.22


Macromolecule Entities
Molecule Chains Length Organism Details
RIBOSOMAL PROTEIN S2 B 256 Thermus thermophilus Gene Name(s): rpsB rps2 TTHA0861
RIBOSOMAL PROTEIN S3 C 239 Thermus thermophilus Gene Name(s): rpsC rps3 TTHA1686
RIBOSOMAL PROTEIN S4 D 209 Thermus thermophilus Gene Name(s): rpsD rps4 TTHA1665
RIBOSOMAL PROTEIN S5 E 162 Thermus thermophilus Gene Name(s): rpsE TTHA1675
RIBOSOMAL PROTEIN S6 F 101 Thermus thermophilus Gene Name(s): rpsF TTHA0245
RIBOSOMAL PROTEIN S7 G 156 Thermus thermophilus Gene Name(s): rpsG rps7 TTHA1696
RIBOSOMAL PROTEIN S8 H 138 Thermus thermophilus Gene Name(s): rpsH TTHA1678
RIBOSOMAL PROTEIN S9 I 128 Thermus thermophilus Mutation: H58R
Gene Name(s): rpsI rps9 TTHA1464
RIBOSOMAL PROTEIN S10 J 105 Thermus thermophilus Gene Name(s): rpsJ TTHA1693
RIBOSOMAL PROTEIN S11 K 129 Thermus thermophilus Gene Name(s): rpsK rps11 TTHA1666
RIBOSOMAL PROTEIN S12 L 135 Thermus thermophilus Gene Name(s): rpsL TTHA1697
RIBOSOMAL PROTEIN S13 M 126 Thermus thermophilus Gene Name(s): rpsM rps13 TTHA1667
RIBOSOMAL PROTEIN S14 N 61 Thermus thermophilus Gene Name(s): rpsZ rpsN TTHA1679
RIBOSOMAL PROTEIN S15 O 89 Thermus thermophilus Gene Name(s): rpsO TTHA1138
RIBOSOMAL PROTEIN S16 P 88 Thermus thermophilus Gene Name(s): rpsP TTHA1035
RIBOSOMAL PROTEIN S17 Q 105 Thermus thermophilus Mutation: E96Q
Gene Name(s): rpsQ TTHA1683
RIBOSOMAL PROTEIN S18 R 88 Thermus thermophilus Gene Name(s): rpsR TTHA0243
RIBOSOMAL PROTEIN S19 S 93 Thermus thermophilus Gene Name(s): rpsS TTHA1688
RIBOSOMAL PROTEIN S20 T 106 Thermus thermophilus Mutation: I41V
Gene Name(s): rpsT rps20 TTHA1397
RIBOSOMAL PROTEIN THX V 27 Thermus thermophilus Gene Name(s): rpsU TTHA1396
Macromolecule Entities
Molecule Chains Length Organism Details
16S RIBOSOMAL RNA A 1523 Thermus thermophilus CHAIN A (16S RNA) HAS E. COLI NUMBERING
ANTICODON STEM-LOOP OF TRANSFER RNA WITH ANTICODON CCCG X 4 synthetic SEQUENCE BASED ON E.COLI TRNAPHE WITH ANTICODON SUBSTITUTED WITH CCCG
A-SITE MESSENGER RNA FRAGMENT CGGG Y 18 synthetic

Small Molecules
Ligands 4 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
K
Query on K

G POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
Ligand Explorer
 
JSmol
MG
Query on MG

G 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

G ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
Ligand Explorer
 
JSmol

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.2 Å
  • R-Value Free: 0.282
  • R-Value Work: 0.238
  • Space Group: P 41 21 2
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 401.90 α = 90.00
b = 401.90 β = 90.00
c = 174.43 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2007-03-28
  • Released Date: 2007-10-02
  • Deposition author(s): Dunham, C.M., Selmer, M., Phelps, S.S., Kelley, A.C., Suzuki, T., Joseph, S., Ramakrishnan, V.

Revision History

  • 2012-10-10
    Type: Biological assembly | Details: REMARK 300, REMARK 350
  • 2012-09-19
    Type: Binding sites and description | Details: REMARK 800
  • 2012-09-19
    Type: Non-polymer description | Details: HET,HETSYN,REMARK 620
  • 2012-09-19
    Type: Linkage | Details: CONECT,LINK
  • 2012-09-19
    Type: Other | Details: MASTER
  • 2012-09-19
    Type: Atom nomenclature | Details: HETATM
  • 2012-09-19
    Type: Biological assembly | Details: REMARK 350
  • 2012-09-19
    Type: Version format compliance | Details: REMARK 4