3A74

Lysyl-tRNA synthetase from Bacillus stearothermophilus complexed with Diadenosine Tetraphosphate (AP4A)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Free: 0.228 
  • R-Value Work: 0.207 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Crystal Structure of Lysyl-tRNA Synthetase from Bacillus stearothermophilus in Complex with Diadenosine Tetraphosphate (AP4A): Insights into AP4A Synthesis Mechanisms and Implication for Recognition of Discriminator Base of tRNA^Lys

Sakurama, H.Takita, T.Mikami, B.Itoh, T.Yasukawa, K.Inouye, K.

To be published.

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Lysyl-tRNA synthetase
A, B, C, D
493Geobacillus stearothermophilusGene Names: lysS
EC: 6.1.1.6
Find proteins for Q9RHV9 (Geobacillus stearothermophilus)
Go to UniProtKB:  Q9RHV9
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
LYN
Query on LYN

Download SDF File 
Download CCD File 
A, B, C, D
2,6-DIAMINO-HEXANOIC ACID AMIDE
C6 H16 N3 O
HKXLAGBDJVHRQG-YFKPBYRVSA-O
 Ligand Interaction
MG
Query on MG

Download SDF File 
Download CCD File 
A, B, C, D
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
B4P
Query on B4P

Download SDF File 
Download CCD File 
A, B, C, D
BIS(ADENOSINE)-5'-TETRAPHOSPHATE
C20 H28 N10 O19 P4
YOAHKNVSNCMZGQ-XPWFQUROSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Free: 0.228 
  • R-Value Work: 0.207 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 80.176α = 90.00
b = 85.080β = 90.01
c = 151.764γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data reduction
CNSrefinement
DENZOdata reduction
HKL-2000data scaling
CNSphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2010-09-22
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance