spacer
spacer

PDBsum entry 2blp

Go to PDB code: 
protein metals links
Hydrolase PDB id
2blp
Jmol
Contents
Protein chain
124 a.a. *
Metals
_CL
Waters ×143
* Residue conservation analysis
PDB id:
2blp
Name: Hydrolase
Title: Rnase before unattenuated x-ray burn
Structure: Ribonuclease pancreatic precursor. Chain: a. Synonym: rnase 1, rnase a. Ec: 3.1.27.5
Source: Bos taurus. Bovine. Organism_taxid: 9913. Organ: pancreas
Resolution:
1.4Å     R-factor:   0.147     R-free:   0.176
Authors: M.H.Nanao,R.B.Ravelli
Key ref:
M.H.Nanao et al. (2005). Improving radiation-damage substructures for RIP. Acta Crystallogr D Biol Crystallogr, 61, 1227-1237. PubMed id: 16131756 DOI: 10.1107/S0907444905019360
Date:
08-Mar-05     Release date:   07-Sep-05    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
P61823  (RNAS1_BOVIN) -  Ribonuclease pancreatic
Seq:
Struc:
150 a.a.
124 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class: E.C.3.1.27.5  - Pancreatic ribonuclease.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: Endonucleolytic cleavage to nucleoside 3'-phosphates and 3'-phosphooligonucleotides ending in C-P or U-P with 2',3'-cyclic phosphate intermediates.
 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     extracellular region   1 term 
  Biological process     metabolic process   3 terms 
  Biochemical function     nucleic acid binding     6 terms  

 

 
DOI no: 10.1107/S0907444905019360 Acta Crystallogr D Biol Crystallogr 61:1227-1237 (2005)
PubMed id: 16131756  
 
 
Improving radiation-damage substructures for RIP.
M.H.Nanao, G.M.Sheldrick, R.B.Ravelli.
 
  ABSTRACT  
 
Specific radiation damage can be used to solve macromolecular structures using the radiation-damage-induced phasing (RIP) method. The method has been investigated for six disulfide-containing test structures (elastase, insulin, lysozyme, ribonuclease A, trypsin and thaumatin) using data sets that were collected on a third-generation synchrotron undulator beamline with a highly attenuated beam. Each crystal was exposed to the unattenuated X-ray beam between the collection of a 'before' and an 'after' data set. The X-ray 'burn'-induced intensity differences ranged from 5 to 15%, depending on the protein investigated. X-ray-susceptible substructures were determined using the integrated direct and Patterson methods in SHELXD. The best substructures were found by downscaling the 'after' data set in SHELXC by a scale factor K, with optimal values ranging from 0.96 to 0.99. The initial substructures were improved through iteration with SHELXE by the addition of negatively occupied sites as well as a large number of relatively weak sites. The final substructures ranged from 40 to more than 300 sites, with strongest peaks as high as 57sigma. All structures except one could be solved: it was not possible to find the initial substructure for ribonuclease A, however, SHELXE iteration starting with the known five most susceptible sites gave excellent maps. Downscaling proved to be necessary for the solution of elastase, lysozyme and thaumatin and reduced the number of SHELXE iterations in the other cases. The combination of downscaling and substructure iteration provides important benefits for the phasing of macromolecular structures using radiation damage.
 
  Selected figure(s)  
 
Figure 4.
Figure 4 The effect of scale factor on the structure solution of (a) insulin, (b) lysozyme, (c) thaumatin and (d) trypsin. CC[best] is represented by open squares, wMPE is represented by crosses and pseudo-free CC is represented as closed squares.
Figure 6.
Figure 6 Experimental electron-density maps (a) and weighted mean phase errors (b) for lysozyme for different subsequent iterations in SHELXE. A total of 13 substructure iterations were made; maps were drawn after iteration Nos. 1, 6, 8, 9, 10 and 11.
 
  The above figures are reprinted by permission from the IUCr: Acta Crystallogr D Biol Crystallogr (2005, 61, 1227-1237) copyright 2005.  
  Figures were selected by the author.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
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.  
21444772 R.Sanishvili, D.W.Yoder, S.B.Pothineni, G.Rosenbaum, S.Xu, S.Vogt, S.Stepanov, O.A.Makarov, S.Corcoran, R.Benn, V.Nagarajan, J.L.Smith, and R.F.Fischetti (2011).
Radiation damage in protein crystals is reduced with a micron-sized X-ray beam.
  Proc Natl Acad Sci U S A, 108, 6127-6132.  
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.  
20383001 G.M.Sheldrick (2010).
Experimental phasing with SHELXC/D/E: combining chain tracing with density modification.
  Acta Crystallogr D Biol Crystallogr, 66, 479-485.  
20382994 G.P.Bourenkov, and A.N.Popov (2010).
Optimization of data collection taking radiation damage into account.
  Acta Crystallogr D Biol Crystallogr, 66, 409-419.  
20516626 K.Diederichs (2010).
Quantifying instrument errors in macromolecular X-ray data sets.
  Acta Crystallogr D Biol Crystallogr, 66, 733-740.  
19836331 P.B.Moore (2009).
On the relationship between diffraction patterns and motions in macromolecular crystals.
  Structure, 17, 1307-1315.  
18156677 G.M.Sheldrick (2008).
A short history of SHELX.
  Acta Crystallogr A, 64, 112-122.  
17959373 T.De la Mora-Rey, and C.M.Wilmot (2007).
Synergy within structural biology of single crystal optical spectroscopy and X-ray crystallography.
  Curr Opin Struct Biol, 17, 580-586.  
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.