6BQZ | pdb_00006bqz

Crystal Structure of Tyrosine-tRNA Synthetase from Acinetobacter baumannii with bound L-Tyrosine

• PDB DOI: https://doi.org/10.2210/pdb6BQZ/pdb

• Classification: LIGASE
• Organism(s): Acinetobacter baumannii
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2017-11-29 Released: 2017-12-13 
• Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease (SSGCID)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 
  0.231 (Depositor), 0.235 (DCC) 
• R-Value Work: 
  0.180 (Depositor), 0.184 (DCC) 
• R-Value Observed: 
  0.184 (Depositor) 

Starting Model: experimental

Literature

Crystal Structure of Tyrosine-tRNA Synthetase from Acinetobacter baumannii with bound L-Tyrosine

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

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 91.06 kDa 
• Atom Count: 3,524 
• Modeled Residue Count: 430 
• Deposited Residue Count: 816 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Tyrosine--tRNA ligase	A, B	408	Acinetobacter baumannii	Mutation(s): 0  Gene Names:  tyrS, A7A59_01455, A7A65_06465, A7M79_16285, A7M90_19385, A7N09_15205, APD06_07635, APD31_16655, B9X91_04915, B9X95_11600, BGC29_18795, BWP00_10095, CAS83_08605, CBI29_00001, IX87_14380, LV38_03496 EC: 6.1.1.1
UniProt
Find proteins for B0VML7 (Acinetobacter baumannii (strain SDF)) Explore B0VML7  Go to UniProtKB:  B0VML7

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
TYR	C [auth A], E [auth B]	TYROSINE C9 H11 N O3 OUYCCCASQSFEME-QMMMGPOBSA-N
ACT	F [auth B]	ACETATE ION C2 H3 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-M
MG	D [auth A], G [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free:  0.231 (Depositor), 0.235 (DCC) 
• R-Value Work:  0.180 (Depositor), 0.184 (DCC) 
• R-Value Observed: 0.184 (Depositor) 

Diffraction Data: https://doi.org/10.18430/M36BQZ

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 48.26	α = 87.65
b = 49.8	β = 107.11
c = 73.37	γ = 113.86

Software Package:

Software Name	Purpose
XDS	data reduction
XSCALE	data scaling
PHASER	phasing
PHENIX	refinement
PDB_EXTRACT	data extraction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2017-12-13 
Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Revision History  

• Version 1.0: 2017-12-13
  Type: Initial release
  
• Version 1.1: 2024-03-13
  Changes: Data collection, Database references
• Version 1.2: 2026-03-04
  Changes: Refinement description, Structure summary