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PDBsum entry 1n6x
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Hydrolase PDB id
1n6x

 

 

 

 

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Contents
Protein chain
223 a.a. *
Ligands
SO4 ×2
ABN
GOL
Metals
_CA
Waters ×288
* Residue conservation analysis
PDB id:
1n6x
Name: Hydrolase
Title: Rip-phasing on bovine trypsin
Structure: Trypsinogen, cationic. Chain: a. Synonym: beta-trypsin. Ec: 3.4.21.4
Source: Bos taurus. Cattle. Organism_taxid: 9913. Organ: pancreas
Resolution:
1.40Å     R-factor:   0.139     R-free:   0.165
Authors: R.B.G.Ravelli,H.-K.S.Leiros,B.Pan,M.Caffrey,S.Mcsweeney
Key ref:
R.B.Ravelli et al. (2003). Specific radiation damage can be used to solve macromolecular crystal structures. Structure, 11, 217-224. PubMed id: 12575941
Date:
12-Nov-02     Release date:   04-Mar-03    
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.

 

 
Structure 11:217-224 (2003)
PubMed id: 12575941  
 
 
Specific radiation damage can be used to solve macromolecular crystal structures.
R.B.Ravelli, H.K.Leiros, B.Pan, M.Caffrey, S.McSweeney.
 
  ABSTRACT  
 
The use of third generation synchrotron sources has led to renewed concern about the effect of ionizing radiation on crystalline biological samples. In general, the problem is seen as one to be avoided. However, in this paper, it is shown that, far from being a hindrance to successful structure determination, radiation damage provides an opportunity for phasing macromolecular structures. This is successfully demonstrated for both a protein and an oligonucleotide, by way of which complete models were built automatically. The possibility that, through the exploitation of radiation damage, the phase problem could become less of a barrier to macromolecular crystal structure determination is discussed.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
23254650 E.F.Garman, and M.Weik (2013).
Radiation damage to biological macromolecules: some answers and more questions.
  J Synchrotron Radiat, 20, 1-6.  
21525640 D.H.Juers, and M.Weik (2011).
Similarities and differences in radiation damage at 100 K versus 160 K in a crystal of thermolysin.
  J Synchrotron Radiat, 18, 329-337.  
21525645 D.de Sanctis, P.A.Tucker, and S.Panjikar (2011).
Additional phase information from UV damage of selenomethionine labelled proteins.
  J Synchrotron Radiat, 18, 374-380.  
21525638 E.F.Garman, and M.Weik (2011).
Macromolecular crystallography radiation damage research: what's new?
  J Synchrotron Radiat, 18, 313-317.  
20662638 C.Nicolini, and E.Pechkova (2010).
Nanoproteomics for nanomedicine.
  Nanomedicine (Lond), 5, 677-682.  
20382996 D.Borek, M.Cymborowski, M.Machius, W.Minor, and Z.Otwinowski (2010).
Diffraction data analysis in the presence of radiation damage.
  Acta Crystallogr D Biol Crystallogr, 66, 426-436.  
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.  
20382998 M.Schiltz, and G.Bricogne (2010).
'Broken symmetries' in macromolecular crystallography: phasing from unmerged data.
  Acta Crystallogr D Biol Crystallogr, 66, 447-457.  
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.  
21070940 P.Carpentier, A.Royant, M.Weik, and D.Bourgeois (2010).
Raman-assisted crystallography suggests a mechanism of X-ray-induced disulfide radical formation and reparation.
  Structure, 18, 1410-1419.
PDB codes: 2xbr 2xbs
20382995 P.Roversi, S.Johnson, and S.M.Lea (2010).
With phases: how two wrongs can sometimes make a right.
  Acta Crystallogr D Biol Crystallogr, 66, 420-425.  
20382990 T.Beck, T.Gruene, and G.M.Sheldrick (2010).
The magic triangle goes MAD: experimental phasing with a bromine derivative.
  Acta Crystallogr D Biol Crystallogr, 66, 374-380.
PDB codes: 3gt3 3gt4
20567074 Z.Dauter, M.Jaskolski, and A.Wlodawer (2010).
Impact of synchrotron radiation on macromolecular crystallography: a personal view.
  J Synchrotron Radiat, 17, 433-444.  
19240325 J.M.Holton (2009).
A beginner's guide to radiation damage.
  J Synchrotron Radiat, 16, 133-142.  
19390147 M.A.Brooks, R.B.Ravelli, A.A.McCarthy, K.Strub, and S.Cusack (2009).
Structure of SRP14 from the Schizosaccharomyces pombe signal recognition particle.
  Acta Crystallogr D Biol Crystallogr, 65, 421-433.
PDB code: 2w9j
19700309 P.D.Adams, P.V.Afonine, R.W.Grosse-Kunstleve, R.J.Read, J.S.Richardson, D.C.Richardson, and T.C.Terwilliger (2009).
Recent developments in phasing and structure refinement for macromolecular crystallography.
  Curr Opin Struct Biol, 19, 566-572.  
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
19018096 M.Cianci, J.R.Helliwell, and A.Suzuki (2008).
The interdependence of wavelength, redundancy and dose in sulfur SAD experiments.
  Acta Crystallogr D Biol Crystallogr, 64, 1196-1209.
PDB codes: 2w1l 2w1m 2w1x 2w1y
17327667 A.Meents, A.Wagner, R.Schneider, C.Pradervand, E.Pohl, and C.Schulze-Briese (2007).
Reduction of X-ray-induced radiation damage of macromolecular crystals by data collection at 15 K: a systematic study.
  Acta Crystallogr D Biol Crystallogr, 63, 302-309.  
17211076 J.E.McGeehan, P.Carpentier, A.Royant, D.Bourgeois, and R.B.Ravelli (2007).
X-ray radiation-induced damage in DNA monitored by online Raman.
  J Synchrotron Radiat, 14, 99.  
17211072 J.M.Holton (2007).
XANES measurements of the rate of radiation damage to selenomethionine side chains.
  J Synchrotron Radiat, 14, 51-72.  
17582167 V.Oliéric, E.Ennifar, A.Meents, M.Fleurant, C.Besnard, P.Pattison, M.Schiltz, C.Schulze-Briese, and P.Dumas (2007).
Using X-ray absorption spectra to monitor specific radiation damage to anomalously scattering atoms in macromolecular crystallography.
  Acta Crystallogr D Biol Crystallogr, 63, 759-768.  
17057349 A.Wagner, M.Pieren, C.Schulze-Briese, K.Ballmer-Hofer, and A.E.Prota (2006).
Structure determination of VEGF-E by sulfur SAD.
  Acta Crystallogr D Biol Crystallogr, 62, 1430-1434.  
16369095 D.Flot, E.J.Gordon, D.R.Hall, G.A.Leonard, A.McCarthy, J.McCarthy, S.McSweeney, E.Mitchell, D.Nurizzo, R.G.Ravelli, and W.Shepard (2006).
The care and nurture of undulator data sets.
  Acta Crystallogr D Biol Crystallogr, 62, 65-71.  
16421442 H.K.Leiros, J.Timmins, R.B.Ravelli, and S.M.McSweeney (2006).
Is radiation damage dependent on the dose rate used during macromolecular crystallography data collection?
  Acta Crystallogr D Biol Crystallogr, 62, 125-132.
PDB codes: 2bxy 2bxz 2by0 2by1 2by2 2by3 2by5 2by6 2by7 2by8 2by9 2bya
16369100 R.M.Esnouf, C.A.Love, K.Harlos, D.I.Stuart, and E.Y.Jones (2006).
Structure determination of human semaphorin 4D as an example of the use of MAD in non-optimal cases.
  Acta Crystallogr D Biol Crystallogr, 62, 108-115.  
16369088 Z.Dauter (2006).
Current state and prospects of macromolecular crystallography.
  Acta Crystallogr D Biol Crystallogr, 62, 1.  
15917812 B.Gigant, C.Wang, R.B.Ravelli, F.Roussi, M.O.Steinmetz, P.A.Curmi, A.Sobel, and M.Knossow (2005).
Structural basis for the regulation of tubulin by vinblastine.
  Nature, 435, 519-522.
PDB code: 1z2b
15840908 C.Nave, and E.F.Garman (2005).
Towards an understanding of radiation damage in cryocooled macromolecular crystals.
  J Synchrotron Radiat, 12, 257-260.  
15968116 K.Djinović Carugo, J.R.Helliwell, H.Stuhrmann, and M.S.Weiss (2005).
Softer and soft X-rays in macromolecular crystallography.
  J Synchrotron Radiat, 12, 410-419.  
16131756 M.H.Nanao, G.M.Sheldrick, and R.B.Ravelli (2005).
Improving radiation-damage substructures for RIP.
  Acta Crystallogr D Biol Crystallogr, 61, 1227-1237.
PDB codes: 2blo 2blp 2blq 2blr 2blu 2blv 2blw 2blx 2bly 2blz 2bn1 2bn3
15817398 O.Carugo, and K.Djinović Carugo (2005).
When X-rays modify the protein structure: radiation damage at work.
  Trends Biochem Sci, 30, 213-219.  
15840911 R.B.Ravelli, M.H.Nanao, A.Lovering, S.White, and S.McSweeney (2005).
Phasing in the presence of radiation damage.
  J Synchrotron Radiat, 12, 276-284.  
16131763 U.A.Ramagopal, Z.Dauter, R.Thirumuruhan, E.Fedorov, and S.C.Almo (2005).
Radiation-induced site-specific damage of mercury derivatives: phasing and implications.
  Acta Crystallogr D Biol Crystallogr, 61, 1289-1298.  
15036861 E.Pechkova, and C.Nicolini (2004).
Protein nanocrystallography: a new approach to structural proteomics.
  Trends Biotechnol, 22, 117-122.  
15272167 M.Grininger, R.B.Ravelli, U.Heider, and K.Zeth (2004).
Expression, crystallization and crystallographic analysis of DegS, a stress sensor of the bacterial periplasm.
  Acta Crystallogr D Biol Crystallogr, 60, 1429-1431.  
15039557 M.S.Weiss, G.Mander, R.Hedderich, K.Diederichs, U.Ermler, and E.Warkentin (2004).
Determination of a novel structure by a combination of long-wavelength sulfur phasing and radiation-damage-induced phasing.
  Acta Crystallogr D Biol Crystallogr, 60, 686-695.
PDB code: 1sau
15159561 M.Schiltz, P.Dumas, E.Ennifar, C.Flensburg, W.Paciorek, C.Vonrhein, and G.Bricogne (2004).
Phasing in the presence of severe site-specific radiation damage through dose-dependent modelling of heavy atoms.
  Acta Crystallogr D Biol Crystallogr, 60, 1024-1031.  
15502302 P.H.Zwart, S.Banumathi, M.Dauter, and Z.Dauter (2004).
Radiation-damage-induced phasing with anomalous scattering: substructure solution and phasing.
  Acta Crystallogr D Biol Crystallogr, 60, 1958-1963.  
15026418 R.Kort, K.J.Hellingwerf, and R.B.Ravelli (2004).
Initial events in the photocycle of photoactive yellow protein.
  J Biol Chem, 279, 26417-26424.
PDB codes: 1uwn 1uwp
15159568 S.Banumathi, P.H.Zwart, U.A.Ramagopal, M.Dauter, and Z.Dauter (2004).
Structural effects of radiation damage and its potential for phasing.
  Acta Crystallogr D Biol Crystallogr, 60, 1085-1093.  
15341736 V.Adam, A.Royant, V.Nivière, F.P.Molina-Heredia, and D.Bourgeois (2004).
Structure of superoxide reductase bound to ferrocyanide and active site expansion upon X-ray-induced photo-reduction.
  Structure, 12, 1729-1740.
PDB codes: 1vzg 1vzh 1vzi
14573944 E.Garman, and J.W.Murray (2003).
Heavy-atom derivatization.
  Acta Crystallogr D Biol Crystallogr, 59, 1903-1913.  
12876345 G.Evans, M.Polentarutti, K.Djinovic Carugo, and G.Bricogne (2003).
SAD phasing with triiodide, softer X-rays and some help from radiation damage.
  Acta Crystallogr D Biol Crystallogr, 59, 1429-1434.  
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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