2UXC

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

Structural Biology Knowledgebase: 2UXC SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.9 Å
  • R-Value Free: 0.255
  • R-Value Work: 0.217

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 2UXC

Classification: RIBOSOME

Total Structure Weight: 797411.69


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 U 27 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 CHAIN A (16S RNA) HAS E. COLI NUMBERING
A-SITE MESSENGER RNA FRAGMENT CGGG X 18 Synthetic construct
ANTICODON STEM-LOOP OF TRANSFER RNA WITH ANTICODON ACGA Y 5 Synthetic construct SEQUENCE BASED ON E.COLI TRNAPHE WITH EXTENDED ANTICODON

Small Molecules
Ligands 4 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

A ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
K
Query on K

A POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
MG
Query on MG

A MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.9 Å
  • R-Value Free: 0.255
  • R-Value Work: 0.217
  • Space Group: P 41 21 2
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 401.82 α = 90.00
b = 401.82 β = 90.00
c = 175.10 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2007-03-28
  • Released Date: 2007-05-08
  • Deposition author(s): Dunham, C.M., Selmer, M., Phelps, S.S., Kelley, A.C., Suzuki, T., Joseph, S., Ramakrishnan, V.

Revision History

  • 2015-05-27
    Type: Sequence database correspondence | Details: DBREF
  • 2015-05-20
    Type: Atom nomenclature | Details: ATOM
  • 2015-05-20
    Type: Other | Details: TER
  • 2015-05-20
    Type: Version format compliance | Details: REMARK 4
  • 2015-05-20
    Type: Data collection | Details: REMARK 200
  • 2015-05-20
    Type: Refinement description | Details: REMARK 3
  • 2015-05-20
    Type: Biological assembly | Details: REMARK 350