3A74

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.228 
  • R-Value Work: 0.207 
  • R-Value Observed: 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:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Lysyl-tRNA synthetaseA, B, C, D493Geobacillus stearothermophilusMutation(s): 0 
Gene Names: lysS
EC: 6.1.1.6
Find proteins for Q9RHV9 (Geobacillus stearothermophilus)
Explore Q9RHV9 
Go to UniProtKB:  Q9RHV9
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
B4P
Query on B4P

Download Ideal Coordinates CCD File 
E [auth A], J [auth B], O [auth C], T [auth D]BIS(ADENOSINE)-5'-TETRAPHOSPHATE
C20 H28 N10 O19 P4
YOAHKNVSNCMZGQ-XPWFQUROSA-N
 Ligand Interaction
LYN
Query on LYN

Download Ideal Coordinates CCD File 
F [auth A], K [auth B], P [auth C], U [auth D]2,6-DIAMINO-HEXANOIC ACID AMIDE
C6 H16 N3 O
HKXLAGBDJVHRQG-YFKPBYRVSA-O
 Ligand Interaction
MG
Query on MG

Download Ideal Coordinates CCD File 
G [auth A] , H [auth A] , I [auth A] , L [auth B] , M [auth B] , N [auth B] , Q [auth C] , R [auth C] , 
G [auth A],  H [auth A],  I [auth A],  L [auth B],  M [auth B],  N [auth B],  Q [auth C],  R [auth C],  S [auth C],  V [auth D],  W [auth D],  X [auth D]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.228 
  • R-Value Work: 0.207 
  • R-Value Observed: 0.207 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 80.176α = 90
b = 85.08β = 90.01
c = 151.764γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
CNSrefinement
HKL-2000data reduction
HKL-2000data scaling
CNSphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

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