2APR

STRUCTURE AND REFINEMENT AT 1.8 ANGSTROMS RESOLUTION OF THE ASPARTIC PROTEINASE FROM RHIZOPUS CHINENSIS


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Structure and refinement at 1.8 A resolution of the aspartic proteinase from Rhizopus chinensis.

Suguna, K.Bott, R.R.Padlan, E.A.Subramanian, E.Sheriff, S.Cohen, G.H.Davies, D.R.

(1987) J.Mol.Biol. 196: 877-900


  • PubMed Abstract: 
  • The structure of rhizopuspepsin (EC 3.4.23.6), the aspartic proteinase from Rhizopus chinensis, has been refined to a crystallographic R-factor of 0.143 at 1.8 A resolution. The positions of 2417 protein atoms have been determined with a root-mean-sq ...

    The structure of rhizopuspepsin (EC 3.4.23.6), the aspartic proteinase from Rhizopus chinensis, has been refined to a crystallographic R-factor of 0.143 at 1.8 A resolution. The positions of 2417 protein atoms have been determined with a root-mean-square (r.m.s.) error of 0.12 A. In the final model, the r.m.s. deviation from ideality for bond distances is 0.010 A, and for angle distances it is 0.034 A. During the course of the refinement, a calcium ion and 373 water molecules, of which 17 are internal, have been located. The active aspartate residues, Asp35 and Asp218, are involved in similar hydrogen-bonding interactions with neighboring residues and with several water molecules. One water molecule is located between the two carboxyl groups of the catalytic aspartate residues in a tightly hydrogen-bonded position. The refinement resulted in an unambiguous interpretation of the highly mobile "flap", a beta-hairpin loop region that projects over the binding pocket. Large solvent channels are formed when the molecules pack in the crystal, exposing the binding pocket and making it easily accessible. Intermolecular contacts involve mainly solvent molecules and a few protein atoms. The three-dimensional structure of rhizopuspepsin closely resembles other aspartic proteinase structures. A detailed comparison with the structure of penicillopepsin showed striking similarities as well as subtle differences in the active site geometry and molecular packing.


    Related Citations: 
    • Homology Among Acid Proteases. Comparison of Crystal Structures at 3 Angstroms Resolution of Acid Proteases from Rhizopus Chinensis and Endothia Parasitica
      Subramanian, E.,Swan, I.D.A.,Liu, M.,Davies, D.R.,Jenkins, J.A.,Tickle, I.J.,Blundell, T.L.
      (1977) Proc.Natl.Acad.Sci.USA 74: 556
    • Three-Dimensional Structure of the Complex of the Rhizopus Chinensis Carboxyl Proteinase and Pepstatin at 2.5 Angstroms Resolution
      Bott, R.R.,Subramanian, E.,Davies, D.R.
      (1982) Biochemistry 21: 6956
    • The Crystal Structure of an Acid Protease from Rhizopus Chinensis at 2.5 Angstroms Resolution
      Subramanian, E.,Liu, M.,Swan, I.D.A.,Davies, D.R.
      (1977) Adv.Exp.Med.Biol. 95: 33


    Organizational Affiliation

    Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, Bethesda, MD 20892.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
RHIZOPUSPEPSIN
A
325Rhizopus chinensisMutation(s): 0 
EC: 3.4.23.21
Find proteins for P06026 (Rhizopus chinensis)
Go to UniProtKB:  P06026
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: 1.8 Å
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 60.310α = 90.00
b = 60.600β = 90.00
c = 106.970γ = 90.00
Software Package:
Software NamePurpose
PROLSQrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 1987-03-19 
  • Released Date: 1987-07-16 
  • Deposition Author(s): Suguna, K., Davies, D.R.
  • This entry supersedes: 1APR

Revision History 

  • Version 1.0: 1987-07-16
    Type: Initial release
  • Version 1.1: 2008-03-03
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance
  • Version 1.3: 2017-11-29
    Type: Derived calculations, Other