4JYZ

Crystal structure of E. coli glutaminyl-tRNA synthetase bound to ATP and native tRNA(Gln) containing the cmnm5s2U34 anticodon wobble base

Structural Biology Knowledgebase: 4JYZ SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.263
  • R-Value Work: 0.234

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 4JYZ

Classification: ligase / rna

Total Structure Weight: 88371.30


Macromolecule Entities
Molecule Chains Length Organism Details
Glutamine--tRNA ligase A 553 Escherichia coli EC#: 6.1.1.18 IUBMB
Gene Name(s): glnS b0680 JW0666
Macromolecule Entities
Molecule Chains Length Organism Details
RNA (72-MER) B 75 Escherichia coli

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

A ADENOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O13 P3
ZKHQWZAMYRWXGA-KQYNXXCUSA-N
Ligand Explorer
 
JSmol
SO4
Query on SO4

A SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
Ligand Explorer
 
JSmol
Modified Residues 8 Unique
ID Chains Type Formula 2D Diagram Parent
4SU
Query on 4SU
B RNA LINKING C9 H13 N2 O8 P S U
OMG
Query on OMG
B RNA LINKING C11 H16 N5 O8 P G
H2U
Query on H2U
B RNA LINKING C9 H15 N2 O9 P U
OMU
Query on OMU
B RNA LINKING C10 H15 N2 O9 P U
1RN
Query on 1RN
B RNA LINKING C12 H16 N3 O10 P S U
2MA
Query on 2MA
B RNA LINKING C11 H16 N5 O7 P A
PSU
Query on PSU
B RNA LINKING C9 H13 N2 O9 P U
5MU
Query on 5MU
B RNA LINKING C10 H15 N2 O9 P U

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.263
  • R-Value Work: 0.234
  • Space Group: C 2 2 21
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 93.40 α = 90.00
b = 234.62 β = 90.00
c = 113.70 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2013-04-01
  • Released Date: 2013-05-29
  • Deposition author(s): Perona, J.J., Rodriguez-Hernandez, A.

Revision History

  • 2013-10-23
    Type: Citation | Details: Citation update
  • 2013-08-21
    Type: Citation | Details: Citation update