2PRK

SYNCHROTRON X-RAY DATA COLLECTION AND RESTRAINED LEAST-SQUARES REFINEMENT OF THE CRYSTAL STRUCTURE OF PROTEINASE K AT 1.5 ANGSTROMS RESOLUTION


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.5 Å

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Synchrotron X-ray data collection and restrained least-squares refinement of the crystal structure of proteinase K at 1.5 A resolution.

Betzel, C.Pal, G.P.Saenger, W.

(1988) Acta Crystallogr.,Sect.B 44: 163-172

  • DOI: 10.1107/s010876818700939x

  • PubMed Abstract: 
  • The structure of the serine endopeptidase proteinase K (279 amino acid residues; 28,790 daltons) has been refined by restrained least-squares methods to a conventional R value of 16.7% employing synchrotron film data of 30,812 reflections greater tha ...

    The structure of the serine endopeptidase proteinase K (279 amino acid residues; 28,790 daltons) has been refined by restrained least-squares methods to a conventional R value of 16.7% employing synchrotron film data of 30,812 reflections greater than 3 sigma in the 5.0 to 1.5 A resolution range. During refinement, the molecular structure was restrained to known stereochemistry, with root-mean-square (r.m.s.) deviation of 0.015 A from ideal bond lengths. The average atomic temperature factor, B, is 11.1 A2 for all atoms. The final model comprises 2020 protein atoms and 174 solvent molecules (which were given unit occupancies). Four corrections to the amino acid sequence were made, which were confirmed later by sequence analysis of the proteinase K gene: a deletion of one glycine in position 80; a change of sequence in position 207-208 and insertions of the dipeptide 210-211 and of residue 270. The r.m.s. deviation in the alpha-C atomic positions between the final refined model and the initial model built on the basis of a 3.3 A mini-map is 1.72 A for 227 out of 266 residues, which were originally traced in the mini-map without sequence information. The positions of the remaining 39 residues deviate by more than 8 A from the original ones and are located in regions where extensive revision of the structural model was necessary.


    Related Citations: 
    • Crystallization of the Bifunctional Proteinase/Amylase Inhibitor Pki-3 and of its Complex with Proteinase K
      Pal, G.P.,Betzel, C.,Jany, K.-D.,Saenger, W.
      (1986) FEBS Lett. 197: 111
    • Three-Dimensional Structure of Fungal Proteinase K Reveals Similarity to Bacterial Subtilisin
      Paehler, A.,Banerjee, A.,Dattagupta, J.K.,Fujiwara, T.,Lindner, K.,Pal, G.P.,Suck, D.,Weber, G.,Saenger, W.
      (1984) Embo J. 3: 1311
    • Crystallization of the Fungal Enzyme Proteinase K and Amino Acid Composition
      Dattagupta, J.K.,Fujiwara, T.,Grishin, E.V.,Lindner, K.,Manor, P.C.,Pieniazek, N.J.,Saenger, W.,Suck, D.
      (1975) J.Mol.Biol. 97: 267
    • Active-Site Geometry of Proteinase K. Crystallographic Study of its Complex with a Dipeptide Chloromethyl Ketone Inhibitor
      Betzel, C.,Pal, G.P.,Struck, M.,Jany, K.-D.,Saenger, W.
      (1986) FEBS Lett. 197: 105


    Organizational Affiliation

    Institut für Kristallographie, Freie Universität Berlin, Federal Republic of Germany.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
PROTEINASE K
A
279Parengyodontium albumMutation(s): 0 
Gene Names: PROK
EC: 3.4.21.64
Find proteins for P06873 (Parengyodontium album)
Go to UniProtKB:  P06873
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
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.5 Å
  • Space Group: P 43 21 2
Unit Cell:
Length (Å)Angle (°)
a = 68.170α = 90.00
b = 68.170β = 90.00
c = 108.260γ = 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: 1988-04-16
    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