3UNR

Bond length analysis of asp, glu and his residues in trypsin at 1.2A resolution


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.2 Å
  • R-Value Free: 0.121 
  • R-Value Work: 0.105 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Protonation-state determination in proteins using high-resolution X-ray crystallography: effects of resolution and completeness.

Fisher, S.J.Blakeley, M.P.Cianci, M.McSweeney, S.Helliwell, J.R.

(2012) Acta Crystallogr.,Sect.D 68: 800-809

  • DOI: 10.1107/S0907444912012589
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • A bond-distance analysis has been undertaken to determine the protonation states of ionizable amino acids in trypsin, subtilisin and lysozyme. The diffraction resolutions were 1.2 Å for trypsin (97% complete, 12% H-atom visibility at 2.5σ), 1.26 Å fo ...

    A bond-distance analysis has been undertaken to determine the protonation states of ionizable amino acids in trypsin, subtilisin and lysozyme. The diffraction resolutions were 1.2 Å for trypsin (97% complete, 12% H-atom visibility at 2.5σ), 1.26 Å for subtilisin (100% complete, 11% H-atom visibility at 2.5σ) and 0.65 Å for lysozyme (PDB entry 2vb1; 98% complete, 30% H-atom visibility at 3σ). These studies provide a wide diffraction resolution range for assessment. The bond-length e.s.d.s obtained are as small as 0.008 Å and thus provide an exceptional opportunity for bond-length analyses. The results indicate that useful information can be obtained from diffraction data at around 1.2-1.3 Å resolution and that minor increases in resolution can have significant effects on reducing the associated bond-length standard deviations. The protonation states in histidine residues were also considered; however, owing to the smaller differences between the protonated and deprotonated forms it is much more difficult to infer the protonation states of these residues. Not even the 0.65 Å resolution lysozyme structure provided the necessary accuracy to determine the protonation states of histidine.


    Organizational Affiliation

    School of Chemistry, University of Manchester, Brunswick Street, Manchester M13 9PL, England. fisher@ill.fr




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Cationic trypsin
A
223Bos taurusMutation(s): 0 
EC: 3.4.21.4
Find proteins for P00760 (Bos taurus)
Go to UniProtKB:  P00760
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download SDF File 
Download CCD File 
A
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
GOL
Query on GOL

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Download CCD File 
A
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
CA
Query on CA

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Download CCD File 
A
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
BEN
Query on BEN

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Download CCD File 
A
BENZAMIDINE
C7 H8 N2
PXXJHWLDUBFPOL-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.2 Å
  • R-Value Free: 0.121 
  • R-Value Work: 0.105 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 54.357α = 90.00
b = 58.079β = 90.00
c = 66.899γ = 90.00
Software Package:
Software NamePurpose
MOSFLMdata reduction
PHENIXrefinement
SCALAdata scaling
MLPHAREphasing
MxCuBEdata collection

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2012-06-27
    Type: Initial release
  • Version 1.1: 2013-01-23
    Type: Database references