5PTP

STRUCTURE OF HYDROLASE (SERINE PROTEINASE)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.34 Å
  • R-Value Work: 0.152 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Solvent structure in crystals of trypsin determined by X-ray and neutron diffraction.

Finer-Moore, J.S.Kossiakoff, A.A.Hurley, J.H.Earnest, T.Stroud, R.M.

(1992) Proteins 12: 203-222

  • DOI: 10.1002/prot.340120302

  • PubMed Abstract: 
  • The solvent structure in orthorhombic crystals of bovine trypsin has been independently determined by X-ray diffraction to 1.35 A resolution and by neutron diffraction to 2.1 A resolution. A consensus model of the water molecule positions was obtaine ...

    The solvent structure in orthorhombic crystals of bovine trypsin has been independently determined by X-ray diffraction to 1.35 A resolution and by neutron diffraction to 2.1 A resolution. A consensus model of the water molecule positions was obtained using oxygen positions identified in the electron density map determined by X-ray diffraction, which were verified by comparison to D2O-H2O difference neutron scattering density. Six of 184 water molecules in the X-ray structure, all with B-factors greater than 50 A2, were found to be spurious after comparison with neutron results. Roughly two-thirds of the water of hydration expected from thermodynamic data for proteins was localized by neutron diffraction; approximately one-half of the water of hydration was located by X-ray diffraction. Polar regions of the protein are well hydrated, and significant D2O-H2O difference density is seen for a small number of water molecules in a second shell of hydration. Hydrogen bond lengths and angles calculated from unconstrained refinement of water positions are distributed about values typically seen in small molecule structures. Solvent models found in seven other bovine trypsin and trypsinogen and rat trypsin structures determined by X-ray diffraction were compared. Internal water molecules are well conserved in all trypsin structures including anionic rat trypsin, which is 65% homologous to bovine trypsin. Of the 22 conserved waters in trypsin, 19 were also found in trypsinogen, suggesting that they are located in regions of the apoprotein that are structurally conserved in the transition to the mature protein. Seven waters were displaced upon activation of trypsinogen. Water structure at crystal contacts is not generally conserved in different crystal forms. Three groups of integral structural water molecules are highly conserved in all solvent structures, including a spline of water molecules inserted between two beta-strands, which may resemble an intermediate in the formation of beta sheets during the folding of a protein.


    Related Citations: 
    • The Crystal and Molecular Structure of Dip-Inhibited Bovine Trypsin at 2.7 A Resolution
      Stroud, R.M.,Kay, L.M.,Dickerson, R.E.
      (1972) Cold Spring Harbor Symp.Quant.Biol. 36: 125
    • Silver Ion Inhibition of Serine Proteases: Crystallographic Study of Silver-Trypsin
      Chambers, J.L.,Christoph, G.G.,Krieger, M.,Kay, L.,Stroud, R.M.
      (1974) Biochem.Biophys.Res.Commun. 59: 70
    • The Accuracy of Refined Protein Structures, Comparison of Two Independently Refined Models of Bovine Trypsin
      Chambers, J.L.,Stroud, R.M.
      (1979) Acta Crystallogr.,Sect.B 35: 1861
    • Structure and Specific Binding of Trypsin: Comparison of Inhibited Derivatives and a Model for Substrate Binding
      Krieger, M.,Kay, L.M.,Stroud, R.M.
      (1974) J.Mol.Biol. 83: 209
    • The Structure of Bovine Trypsin: Electron Density Maps of the Inhibited Enzyme at 5 a and at 2.7 A Resolution
      Stroud, R.M.,Kay, L.M.,Dickerson, R.E.
      (1974) J.Mol.Biol. 83: 185
    • Structure-Function Relationships in the Serine Proteases
      Stroud, R.M.,Krieger, M.,Koeppe II, R.E.,Kossiakoff, A.A.,Chambers, J.L.
      (1975) PROTEASES AND BIOLOGICAL CONTROL --: 13
    • Difference-Fourier Refinement of the Structure of Dip-Trypsin at 1.5 Angstroms Using a Minicomputer Technique
      Chambers, J.L.,Stroud, R.M.
      (1977) Acta Crystallogr.,Sect.B 33: 1824


    Organizational Affiliation

    Department of Biochemistry and Biophysics, University of California, San Francisco 94143-0448.




Macromolecules

Find similar proteins by: Sequence  |  Structure

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

Download SDF File 
Download CCD File 
A
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
MIS
Query on MIS
A
L-PEPTIDE LINKINGC6 H14 N O6 PSER
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.34 Å
  • R-Value Work: 0.152 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 54.840α = 90.00
b = 58.610β = 90.00
c = 67.470γ = 90.00
Software Package:
Software NamePurpose
PROLSQrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1997-07-07
    Type: Initial release
  • Version 1.1: 2008-03-25
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance
  • Version 1.3: 2017-11-29
    Type: Derived calculations, Other