2CV1 | pdb_00002cv1

Glutamyl-tRNA synthetase from Thermus thermophilus in complex with tRNA(Glu), ATP, and an analog of L-glutamate: a quaternary complex

• PDB DOI: https://doi.org/10.2210/pdb2CV1/pdb
• NAKB: 2CV1

• Classification: ligase/RNA
• Organism(s): Thermus thermophilus
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2005-05-31 Released: 2006-09-05 
• Deposition Author(s): Sekine, S., Yokoyama, S., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.41 Å
• R-Value Free: 
  0.277 (Depositor), 0.260 (DCC) 
• R-Value Work: 
  0.221 (Depositor), 0.210 (DCC) 
• R-Value Observed: 
  0.221 (Depositor) 

Literature

Glutamyl-tRNA synthetase from Thermus thermophilus in complex with tRNA(Glu), ATP, and an analog of L-glutamate: a quaternary complex

Sekine, S., Yokoyama, S.

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly 2  

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

Biological assembly 2 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 157.57 kDa 
• Atom Count: 11,088 
• Modeled Residue Count: 1,086 
• Deposited Residue Count: 1,086 
• Unique protein chains: 1
• Unique nucleic acid chains: 1

Macromolecules

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
glutamyl-tRNA synthetase	C [auth A], D [auth B]	468	Thermus thermophilus	Mutation(s): 0  EC: 6.1.1.17
UniProt
Find proteins for P27000 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)) Explore P27000  Go to UniProtKB:  P27000

Entity ID: 1
Molecule	Chains	Length	Organism	Image
tRNA	A [auth C], B [auth D]	75	N/A

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ATP	I [auth A], L [auth B]	ADENOSINE-5'-TRIPHOSPHATE C10 H16 N5 O13 P3 ZKHQWZAMYRWXGA-KQYNXXCUSA-N
GAU	J [auth A], K [auth A]	(4S)-4-AMINO-5-HYDROXYPENTANOIC ACID C5 H11 N O3 JPYGFLFUDLRNKX-BYPYZUCNSA-N
MG	E [auth C], F [auth C], G [auth D], H [auth D]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.41 Å
• R-Value Free:  0.277 (Depositor), 0.260 (DCC) 
• R-Value Work:  0.221 (Depositor), 0.210 (DCC) 
• R-Value Observed: 0.221 (Depositor) 

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 110.624	α = 90
b = 218.818	β = 90
c = 134.858	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
HKL-2000	data reduction
SCALEPACK	data scaling
CNS	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2006-09-05 
Deposition Author(s): Sekine, S., Yokoyama, S., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

Revision History  

• Version 1.0: 2006-09-05
  Type: Initial release
  
• Version 1.1: 2008-04-30
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 2.0: 2023-11-15
  Changes: Atomic model, Data collection, Database references, Derived calculations