6OTJ

Crystal Structure of Tyrosyl-tRNA synthetase from Neisseria gonorrhoeae with bound L-Tyr


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.85 Å
  • R-Value Free: 0.227 
  • R-Value Work: 0.196 
  • R-Value Observed: 0.197 

Starting Model: experimental
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This is version 1.1 of the entry. See complete history


Literature

Crystal Structure of Tyrosyl-tRNA synthetase from Neisseria gonorrhoeae with bound L-Tyr

Dranow, D.M.Lorimer, D.D.Horanyi, P.S.Edwards, T.E.

To be published.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Tyrosine--tRNA ligase
A, B
439Neisseria gonorrhoeae NCCP11945Mutation(s): 0 
Gene Names: tyrSNGK_0091
EC: 6.1.1.1
UniProt
Find proteins for B4RP13 (Neisseria gonorrhoeae (strain NCCP11945))
Explore B4RP13 
Go to UniProtKB:  B4RP13
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupB4RP13
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
TYR (Subject of Investigation/LOI)
Query on TYR

Download Ideal Coordinates CCD File 
C [auth A],
DA [auth B]
TYROSINE
C9 H11 N O3
OUYCCCASQSFEME-QMMMGPOBSA-N
SO4
Query on SO4

Download Ideal Coordinates CCD File 
BA [auth A]
CA [auth A]
D [auth A]
E [auth A]
EA [auth B]
BA [auth A],
CA [auth A],
D [auth A],
E [auth A],
EA [auth B],
F [auth A],
H [auth A],
HA [auth B],
I [auth A],
IA [auth B],
J [auth A],
K [auth A],
KA [auth B],
L [auth A],
MA [auth B],
N [auth A],
O [auth A],
OA [auth B],
P [auth A],
QA [auth B],
SA [auth B],
TA [auth B],
V [auth A],
W [auth A],
Y [auth A],
YA [auth B],
Z [auth A]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
EDO
Query on EDO

Download Ideal Coordinates CCD File 
AA [auth A]
FA [auth B]
G [auth A]
GA [auth B]
JA [auth B]
AA [auth A],
FA [auth B],
G [auth A],
GA [auth B],
JA [auth B],
LA [auth B],
M [auth A],
NA [auth B],
PA [auth B],
Q [auth A],
R [auth A],
RA [auth B],
S [auth A],
T [auth A],
U [auth A],
UA [auth B],
VA [auth B],
WA [auth B],
X [auth A],
XA [auth B],
ZA [auth B]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

Unit Cell:
Length ( Å )Angle ( ˚ )
a = 121.73α = 90
b = 121.73β = 90
c = 301.81γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XSCALEdata scaling
PDB_EXTRACTdata extraction
MoRDaphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2019-05-15
    Type: Initial release
  • Version 1.1: 2023-10-11
    Changes: Data collection, Database references, Refinement description