5VL1

Crystal Structure of Lysyl-tRNA Synthetase from Mycobacterium ulcerans complexed with L-lysine


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Free: 0.204 
  • R-Value Work: 0.177 
  • R-Value Observed: 0.178 

Starting Model: experimental
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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 Mycobacterium ulcerans complexed with L-lysine

Dranow, D.M.Lorimer, D.D.Edwards, T.E.

To be published.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Lysine--tRNA ligase
A, B, C, D
506Mycobacterium ulcerans Agy99Mutation(s): 0 
Gene Names: lysSMUL_4181
EC: 6.1.1.6
UniProt
Find proteins for A0PV47 (Mycobacterium ulcerans (strain Agy99))
Explore A0PV47 
Go to UniProtKB:  A0PV47
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0PV47
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
PGE
Query on PGE

Download Ideal Coordinates CCD File 
E [auth A],
I [auth B],
L [auth C],
N [auth D]
TRIETHYLENE GLYCOL
C6 H14 O4
ZIBGPFATKBEMQZ-UHFFFAOYSA-N
LYS
Query on LYS

Download Ideal Coordinates CCD File 
F [auth A],
J [auth B],
M [auth C],
O [auth D]
LYSINE
C6 H15 N2 O2
KDXKERNSBIXSRK-YFKPBYRVSA-O
PEG
Query on PEG

Download Ideal Coordinates CCD File 
G [auth A],
H [auth A],
K [auth B]
DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Free: 0.204 
  • R-Value Work: 0.177 
  • R-Value Observed: 0.178 
  • Space Group: P 1
  • Diffraction Data: https://doi.org/10.18430/M35VL1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 95.04α = 90.38
b = 96.69β = 104.84
c = 105.56γ = 117.15
Software Package:
Software NamePurpose
XSCALEdata scaling
PHENIXrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
MoRDaphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2017-05-10
    Type: Initial release
  • Version 1.1: 2023-10-04
    Changes: Data collection, Database references, Refinement description