2SGA

ELECTRON DENSITY CALCULATIONS AS AN EXTENSION OF PROTEIN STRUCTURE REFINEMENT. STREPTOMYCES GRISEUS PROTEASE AT 1.5 ANGSTROMS RESOLUTION


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.5 Å
  • R-Value Work: 0.126 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Electron density calculations as an extension of protein structure refinement. Streptomyces griseus protease A at 1.5 A resolution.

Moult, J.Sussman, F.James, M.N.

(1985) J.Mol.Biol. 182: 555-566


  • PubMed Abstract: 
  • Ab initio quantum mechanical calculations have been used to obtain details of the electron density distribution in a high-resolution refined protein structure. It is shown that with accurate atomic co-ordinates, electron density may be calculated wit ...

    Ab initio quantum mechanical calculations have been used to obtain details of the electron density distribution in a high-resolution refined protein structure. It is shown that with accurate atomic co-ordinates, electron density may be calculated with a quality similar to that which can be obtained directly from crystallographic studies of small organic molecules, and that this density contains information relevant to the understanding of catalysis. Atomic co-ordinates from the 1.8 A and 1.5 A resolution refinements of the crystal structure of protease A from Streptomyces griseus have been used to examine the influence of the environment on the electron density in the side-chain of the active site histidine (His57). The neighbouring aspartic acid 102 is the dominant factor in the environment, and quantum mechanical calculations have been performed on these two residues. Most interesting from the point of view of understanding the catalytic process is the effect that Asp102 has on the electron density in the region of the imidazole nitrogen (N epsilon 2) adjacent to the active site serine 195. In the positively charged imidazolium species, there is a polarization of the N epsilon 2-H bond, reducing the bonding density in a manner that may lower the height of the energy barrier for proton transfer. In the uncharged imidazole species, the proximity of Asp102 causes a movement of density from the lone pair region of the N epsilon 2 into the pi bonding region above and below the plane of the ring. Although it is shown that the primary effect of the aspartic acid is electrostatic, this movement is perpendicular to the direction of the electric field inducing it.


    Related Citations: 
    • Amino Acid Sequence Alignment of Bacterial and Mammalian Pancreatic Serine Proteases Based on Topological Equivalences
      James, M.N.G.,Delbaere, L.T.J.,Brayer, G.D.
      (1978) Can.J.Biochem. 56: 396
    • Tertiary Structural Differences between Microbial Serine Proteases and Pancreatic Serine Enzymes
      Delbaere, L.T.J.,Hutcheon, W.L.B.,James, M.N.G.,Thiessen, W.E.
      (1975) Nature 257: 758
    • Structures of Product and Inhibitor Complexes of Streptomyces Griseus Protease a at 1.8 Angstroms Resolution. A Model for Serine Protease Catalysis
      James, M.N.G.,Sielecki, A.R.,Brayer, G.D.,Delbaere, L.T.J.,Bauer, C.-A.
      (1980) J.Mol.Biol. 144: 43
    • Protein Structure Refinement. Streptomyces Griseus Serine Protease a at 1.8 Angstroms Resolution
      Sielecki, A.R.,Hendrickson, W.A.,Broughton, C.G.,Delbaere, L.T.J.,Brayer, G.D.,James, M.N.G.
      (1979) J.Mol.Biol. 134: 781
    • Molecular Structure of Crystalline Streptomyces Griseus Protease a at 2.8 Angstroms Resolution. II. Molecular Conformation, Comparison with Alpha-Chymotrypsin and Active-Site Geometry
      Brayer, G.D.,Delbaere, L.T.J.,James, M.N.G.
      (1978) J.Mol.Biol. 124: 261
    • Crystallographic and Kinetic Investigations of the Covalent Complex Formed by a Specific Tetrapeptide Aldehyde and the Serine Protease from Streptomyces Griseus
      Brayer, G.D.,Delbaere, L.T.J.,James, M.N.G.,Bauer, C.-A.,Thompson, R.C.
      (1979) Proc.Natl.Acad.Sci.USA 76: 96
    • Structure of the Complex Formed between the Bacterial-Produced Inhibitor Chymostatin and the Serine Enzyme Streptomyces Griseus Protease A
      Delbaere, L.T.J.,Brayer, G.D.
      (1980) J.Mol.Biol. 139: 45
    • Molecular Structure of Crystalline Streptomyces Griseus Protease a at 2.8 Angstroms Resolution. I. Crystallization, Data Collection and Structural Analysis
      Brayer, G.D.,Delbaere, L.T.J.,James, M.N.G.
      (1978) J.Mol.Biol. 124: 243



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
PROTEINASE A
A
181Streptomyces griseusMutation(s): 0 
Gene Names: sprA
EC: 3.4.21.80
Find proteins for P00776 (Streptomyces griseus)
Go to UniProtKB:  P00776
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.5 Å
  • R-Value Work: 0.126 
  • Space Group: P 42
Unit Cell:
Length (Å)Angle (°)
a = 55.120α = 90.00
b = 55.120β = 90.00
c = 54.810γ = 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: 1983-04-21
    Type: Initial release
  • Version 1.1: 2008-03-25
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance