4XKZ | pdb_00004xkz

Crystal structure of the C-terminal anticodon loop binding domain of a valyl-tRNA synthetase from Pseudomonas aeruginosa

• PDB DOI: https://doi.org/10.2210/pdb4XKZ/pdb

• Classification: LIGASE
• Organism(s): Pseudomonas aeruginosa PAO1
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2015-01-12 Released: 2015-02-11 
• Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease (SSGCID)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.95 Å
• R-Value Free: 
  0.193 (Depositor), 0.200 (DCC) 
• R-Value Work: 
  0.156 (Depositor), 0.160 (DCC) 
• R-Value Observed: 
  0.158 (Depositor) 

Literature

Crystal structure of the C-terminal anticodon loop binding domain of a valyl-tRNA synthetase from Pseudomonas aeruginosa.

Edwards, T.E., Fox III, D., Manoil, C.

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 31.54 kDa 
• Atom Count: 2,281 
• Modeled Residue Count: 251 
• Deposited Residue Count: 269 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Valine-tRNA ligase	A	269	Pseudomonas aeruginosa PAO1	Mutation(s): 0  Gene Names: valS, PA3834 EC: 6.1.1.9
UniProt
Find proteins for Q9HXH0 (Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1)) Explore Q9HXH0  Go to UniProtKB:  Q9HXH0

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PGE	F [auth A], G [auth A]	TRIETHYLENE GLYCOL C6 H14 O4 ZIBGPFATKBEMQZ-UHFFFAOYSA-N
IOD	B [auth A], C [auth A], D [auth A], E [auth A]	IODIDE ION I XMBWDFGMSWQBCA-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.95 Å
• R-Value Free:  0.193 (Depositor), 0.200 (DCC) 
• R-Value Work:  0.156 (Depositor), 0.160 (DCC) 
• R-Value Observed: 0.158 (Depositor) 

Diffraction Data: https://doi.org/10.18430/M34XKZ

Space Group: P 4 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 103.36	α = 90
b = 103.36	β = 90
c = 79.14	γ = 90

Software Package:

Software Name	Purpose
XSCALE	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
XDS	data scaling
BALBES	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2015-02-11 
Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Revision History  

• Version 1.0: 2015-02-11
  Type: Initial release
  
• Version 1.1: 2017-11-22
  Changes: Derived calculations, Refinement description, Source and taxonomy
• Version 1.2: 2024-02-28
  Changes: Data collection, Database references, Derived calculations