2APR

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Observed: 0.143 

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

  • DOI: 10.1016/0022-2836(87)90411-6
  • Primary Citation of Related Structures:  
    2APR

  • 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: 
    • 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
    • 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 U S A 74: 556

    Organizational Affiliation

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



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
RHIZOPUSPEPSINA325Rhizopus microsporus var. chinensisMutation(s): 0 
EC: 3.4.23.6 (PDB Primary Data), 3.4.23.21 (UniProt)
Find proteins for P06026 (Rhizopus chinensis)
Explore P06026 
Go to UniProtKB:  P06026
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CA
Query on CA

Download CCD File 
A
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Observed: 0.143 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 60.31α = 90
b = 60.6β = 90
c = 106.97γ = 90
Software Package:
Software NamePurpose
PROLSQrefinement

Structure Validation

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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
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2017-11-29
    Changes: Derived calculations, Other