PDBsum entry 1l0w

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protein Protein-protein interface(s) links
Ligase PDB id
Protein chains
580 a.a. *
Waters ×187
* Residue conservation analysis
PDB id:
Name: Ligase
Title: Aspartyl-tRNA synthetase-1 from space-grown crystals
Structure: Aspartyl-tRNA synthetase. Chain: a, b. Synonym: aspartyl-tRNA synthetase-1, asprs-1, asprs, aspartate--tRNA ligase. Engineered: yes
Source: Thermus thermophilus. Organism_taxid: 274. Expressed in: escherichia coli. Expression_system_taxid: 562
Biol. unit: Dimer (from PQS)
2.01Å     R-factor:   0.217     R-free:   0.246
Authors: J.D.Ng,C.Sauter,B.Lorber,N.Kirkland,J.Arnez,R.Giege
Key ref:
J.D.Ng et al. (2002). Comparative analysis of space-grown and earth-grown crystals of an aminoacyl-tRNA synthetase: space-grown crystals are more useful for structural determination. Acta Crystallogr D Biol Crystallogr, 58, 645-652. PubMed id: 11914489 DOI: 10.1107/S0907444902003177
14-Feb-02     Release date:   20-Mar-02    
Go to PROCHECK summary

Protein chains
Pfam   ArchSchema ?
P36419  (SYD_THETH) -  Aspartate--tRNA(Asp) ligase
580 a.a.
580 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     cytoplasm   1 term 
  Biological process     translation   3 terms 
  Biochemical function     nucleotide binding     6 terms  


DOI no: 10.1107/S0907444902003177 Acta Crystallogr D Biol Crystallogr 58:645-652 (2002)
PubMed id: 11914489  
Comparative analysis of space-grown and earth-grown crystals of an aminoacyl-tRNA synthetase: space-grown crystals are more useful for structural determination.
J.D.Ng, C.Sauter, B.Lorber, N.Kirkland, J.Arnez, R.Giegé.
Protein crystallization under microgravity aims at benefiting from the quasi-absence of convection and sedimentation to favor well ordered crystal nucleation and growth. The dimeric multidomain enzyme aspartyl-tRNA synthetase from Thermus thermophilus has been crystallized within dialysis reactors of the Advanced Protein Crystallization Facility in the laboratory on earth and under microgravity aboard the US Space Shuttle. A strictly comparative crystallographic analysis reveals that the crystals grown in space are superior in every respect to control crystals prepared in otherwise identical conditions on earth. They diffract X-rays more intensely and have a lower mosaicity, facilitating the process of protein structure determination. Indeed, the electron-density map calculated from diffraction data of space-grown crystals contains considerably more detail. The resulting three-dimensional structure model at 2.0 A resolution is more accurate than that produced in parallel using the data originating from earth-grown crystals. The major differences between the structures, including the better defined amino-acid side chains and the higher order of bound water molecules, are emphasized.
  Selected figure(s)  
Figure 1.
Figure 1 Earth-grown (a) and space-grown (b) crystals of AspRS-1. The photographs are on roughly the same scale with crystal dimensions of 1.75 1.25 0.65 mm and 3.0 1.75 1.0 mm, respectively.
Figure 2.
Figure 2 Graph of the diffraction intensities (>, average intensity over estimated error ratio) versus resolution for AspRS-1 crystals. Space-grown crystals showed as much as 40% more intensity in > relative to earth-grown crystals in the resolution range analyzed.
  The above figures are reprinted by permission from the IUCr: Acta Crystallogr D Biol Crystallogr (2002, 58, 645-652) copyright 2002.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
  20944219 D.Das, P.Kozbial, G.W.Han, D.Carlton, L.Jaroszewski, P.Abdubek, T.Astakhova, H.L.Axelrod, C.Bakolitsa, C.Chen, H.J.Chiu, M.Chiu, T.Clayton, M.C.Deller, L.Duan, K.Ellrott, M.A.Elsliger, D.Ernst, C.L.Farr, J.Feuerhelm, A.Grzechnik, J.C.Grant, K.K.Jin, H.A.Johnson, H.E.Klock, M.W.Knuth, S.S.Krishna, A.Kumar, D.Marciano, D.McMullan, M.D.Miller, A.T.Morse, E.Nigoghossian, A.Nopakun, L.Okach, S.Oommachen, J.Paulsen, C.Puckett, R.Reyes, C.L.Rife, N.Sefcovic, H.J.Tien, C.B.Trame, H.van den Bedem, D.Weekes, T.Wooten, Q.Xu, K.O.Hodgson, J.Wooley, A.M.Deacon, A.Godzik, S.A.Lesley, and I.A.Wilson (2010).
The structure of KPN03535 (gi|152972051), a novel putative lipoprotein from Klebsiella pneumoniae, reveals an OB-fold.
  Acta Crystallogr Sect F Struct Biol Cryst Commun, 66, 1254-1260.
PDB code: 3f1z
  17620724 K.Suzuki, Y.Sato, Y.Maeda, S.Shimizu, M.T.Hossain, S.Ubukata, T.Sekiguchi, and A.Takénaka (2007).
Crystallization and preliminary X-ray crystallographic study of a putative aspartyl-tRNA synthetase from the crenarchaeon Sulfolobus tokodaii strain 7.
  Acta Crystallogr Sect F Struct Biol Cryst Commun, 63, 608-612.  
12660169 C.Charron, H.Roy, M.Blaise, R.Giegé, and D.Kern (2003).
Non-discriminating and discriminating aspartyl-tRNA synthetases differ in the anticodon-binding domain.
  EMBO J, 22, 1632-1643.
PDB code: 1n9w
12720277 S.S.Terzyan, C.R.Bourne, P.A.Ramsland, P.C.Bourne, and A.B.Edmundson (2003).
Comparison of the three-dimensional structures of a human Bence-Jones dimer crystallized on Earth and aboard US Space Shuttle Mission STS-95.
  J Mol Recognit, 16, 83-90.
PDB codes: 1lgv 1lhz
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