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PDBsum entry 2by8
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Hydrolase PDB id
2by8

 

 

 

 

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Contents
Protein chain
223 a.a. *
Ligands
BEN
GOL
SO4 ×2
Metals
_CA
Waters ×422
* Residue conservation analysis
PDB id:
2by8
Name: Hydrolase
Title: Is radiation damage dependent on the dose-rate used during macromolecular crystallography data collection
Structure: Cationic trypsin. Chain: x. Synonym: beta-trypsin. Ec: 3.4.21.4
Source: Bos taurus. Organism_taxid: 9913
Resolution:
1.30Å     R-factor:   0.109     R-free:   0.144
Authors: H.-K.S.Leiros,J.Timmins,R.B.G.Ravelli,S.M.Mcsweeney
Key ref:
H.K.Leiros et al. (2006). Is radiation damage dependent on the dose rate used during macromolecular crystallography data collection? Acta Crystallogr D Biol Crystallogr, 62, 125-132. PubMed id: 16421442 DOI: 10.1107/S0907444905033627
Date:
29-Jul-05     Release date:   06-Feb-06    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
P00760  (TRY1_BOVIN) -  Serine protease 1 from Bos taurus
Seq:
Struc: 		246 a.a.
223 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class: E.C.3.4.21.4  - trypsin.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: Preferential cleavage: Arg-|-Xaa, Lys-|-Xaa.

 

 
DOI no: 10.1107/S0907444905033627 Acta Crystallogr D Biol Crystallogr 62:125-132 (2006)
PubMed id: 16421442  
 
 
Is radiation damage dependent on the dose rate used during macromolecular crystallography data collection?
H.K.Leiros, J.Timmins, R.B.Ravelli, S.M.McSweeney.
 
  ABSTRACT  
 
This paper focuses on the radiation-damage effects when applying the same total X-ray dose to protein crystals at different dose rates. These experiments have been performed on both a selenomethionated protein and on bovine trypsin using dose rates that span nearly two orders of magnitude. The results show no clear dose-rate effect on the global indicators of radiation damage, but a small measurable dose-rate effect could be found when studying specific radiation damage. It is hypothesized that this observed dose-rate effect relates to differences in the steady-state free-radical concentration.
 
  Selected figure(s)  
 
Figure 2.
Figure 2 (a) Illustrations of the disulfide bond from Cys395 to the Bme residue and (b) the seven SeMet residues (Mse), with the corresponding vector difference map from the drMTH-Rate75 burn displayed at +4 [sigma] (red) and -4 [sigma] (green). 		Figure 5.
Figure 5 Active site of BT: an illustration of the binding pocket in BT with the vector difference map from BT-Rate24 contoured at +4 [sigma] (red) and -4 [sigma] (green). The inhibitor benzamidine (Bza), Asp189, Ser190, Tyr228 and some surrounding water molecules are shown.
 
  The above figures are reprinted by permission from the IUCr: Acta Crystallogr D Biol Crystallogr (2006, 62, 125-132) copyright 2006.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
21525641 C.Homer, L.Cooper, and A.Gonzalez (2011).
Energy dependence of site-specific radiation damage in protein crystals.
  J Synchrotron Radiat, 18, 338-345.  
21525639 C.Rajendran, F.S.Dworkowski, M.Wang, and C.Schulze-Briese (2011).
Radiation damage in room-temperature data acquisition with the PILATUS 6M pixel detector.
  J Synchrotron Radiat, 18, 318-328.  
21525642 E.De la Mora, I.Carmichael, and E.F.Garman (2011).
Effective scavenging at cryotemperatures: further increasing the dose tolerance of protein crystals.
  J Synchrotron Radiat, 18, 346-357.
PDB codes: 2ybh 2ybi 2ybj 2ybl 2ybm 2ybn 2ydg
21525648 M.Karuppasamy, F.Karimi Nejadasl, M.Vulovic, A.J.Koster, and R.B.Ravelli (2011).
Radiation damage in single-particle cryo-electron microscopy: effects of dose and dose rate.
  J Synchrotron Radiat, 18, 398-412.  
20382986 E.F.Garman (2010).
Radiation damage in macromolecular crystallography: what is it and why should we care?
  Acta Crystallogr D Biol Crystallogr, 66, 339-351.  
20382993 J.M.Holton, and K.A.Frankel (2010).
The minimum crystal size needed for a complete diffraction data set.
  Acta Crystallogr D Biol Crystallogr, 66, 393-408.  
20944242 M.Warkentin, and R.E.Thorne (2010).
Glass transition in thaumatin crystals revealed through temperature-dependent radiation-sensitivity measurements.
  Acta Crystallogr D Biol Crystallogr, 66, 1092-1100.  
18701720 J.P.Colletier, D.Bourgeois, B.Sanson, D.Fournier, J.L.Sussman, I.Silman, and M.Weik (2008).
Shoot-and-Trap: use of specific x-ray damage to study structural protein dynamics by temperature-controlled cryo-crystallography.
  Proc Natl Acad Sci U S A, 105, 11742-11747.
PDB codes: 2vja 2vjb 2vjc 2vjd 2vt6 2vt7
18073104 R.J.Southworth-Davies, M.A.Medina, I.Carmichael, and E.F.Garman (2007).
Observation of decreased radiation damage at higher dose rates in room temperature protein crystallography.
  Structure, 15, 1531-1541.  
The most recent references are shown first. Citation data come partly from CiteXplore and partly from an automated harvesting procedure. Note that this is likely to be only a partial list as not all journals are covered by either method. However, we are continually building up the citation data so more and more references will be included with time. Where a reference describes a PDB structure, the PDB codes are shown on the right.

 

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