3VU8 | pdb_00003vu8

Metionyl-tRNA synthetase from Thermus thermophilus complexed with methionyl-adenylate analogue

• PDB DOI: https://doi.org/10.2210/pdb3VU8/pdb

• Classification: LIGASE
• Organism(s): Thermus thermophilus HB8
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2012-06-22 Released: 2013-06-26 
• Deposition Author(s): Konno, M., Kato-Murayama, M., Toma-Fukai, S., Uchikawa, E., Nureki, O., Yokoyama, S.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 
  0.300 (Depositor), 0.282 (DCC) 
• R-Value Work: 
  0.200 (Depositor), 0.194 (DCC) 
• R-Value Observed: 
  0.205 (Depositor) 

Starting Model: experimental

Literature

The modeling of structures of specific conformation of homosysteine-AMP leading to thiolactone-formation on class Ia aminoacyl-tRNA synthetases

Konno, M., Kato-Murayama, M., Takeda, R., Takasaka, R., Uchikawa, E., Toma-Fukai, S., Ishii, R., Nureki, O., Yokoyama, S.

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 58.76 kDa 
• Atom Count: 4,263 
• Modeled Residue Count: 500 
• Deposited Residue Count: 502 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Methionine--tRNA ligase	A	502	Thermus thermophilus HB8	Mutation(s): 0  Gene Names: metS EC: 6.1.1.10
UniProt
Find proteins for P23395 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)) Explore P23395  Go to UniProtKB:  P23395

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MDS	C [auth A]	N-[METHIONYL]-N'-[ADENOSYL]-DIAMINOSULFONE C15 H24 N8 O6 S2 DAUQVCLMADDCHF-QWRDWHBNSA-N
ZN	B [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free:  0.300 (Depositor), 0.282 (DCC) 
• R-Value Work:  0.200 (Depositor), 0.194 (DCC) 
• R-Value Observed: 0.205 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 50.823	α = 90
b = 82.682	β = 90
c = 120.165	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
X-PLOR	model building
X-PLOR	refinement
SCALEPACK	data scaling
X-PLOR	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2013-06-26 
Deposition Author(s): Konno, M., Kato-Murayama, M., Toma-Fukai, S., Uchikawa, E., Nureki, O., Yokoyama, S.

Revision History  

• Version 1.0: 2013-06-26
  Type: Initial release
  
• Version 1.1: 2023-11-08
  Changes: Data collection, Database references, Derived calculations, Refinement description