1GA6 | pdb_00001ga6

CRYSTAL STRUCTURE ANALYSIS OF PSCP (PSEUDOMONAS SERINE-CARBOXYL PROTEINASE) COMPLEXED WITH A FRAGMENT OF TYROSTATIN (THIS ENZYME RENAMED "SEDOLISIN" IN 2003)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.00 Å
  • R-Value Free: 
    0.131 (Depositor) 
  • R-Value Work: 
    0.123 (Depositor), 0.123 (DCC) 
  • R-Value Observed: 
    0.099 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 1GA6

This is version 1.5 of the entry. See complete history

Literature

Carboxyl proteinase from Pseudomonas defines a novel family of subtilisin-like enzymes.

Wlodawer, A.Li, M.Dauter, Z.Gustchina, A.Uchida, K.Oyama, H.Dunn, B.M.Oda, K.

(2001) Nat Struct Biol 8: 442-446

  • DOI: https://doi.org/10.1038/87610
  • Primary Citation Related Structures: 
    1GA4, 1GA6

  • PubMed Abstract: 

    The crystal structure of a pepstatin-insensitive carboxyl proteinase from Pseudomonas sp. 101 (PSCP) has been solved by single-wavelength anomalous diffraction using the absorption peak of bromide anions. Structures of the uninhibited enzyme and of complexes with an inhibitor that was either covalently or noncovalently bound were refined at 1.0-1.4 A resolution. The structure of PSCP comprises a single compact domain with a diameter of approximately 55 A, consisting of a seven-stranded parallel beta-sheet flanked on both sides by a number of helices. The fold of PSCP is a superset of the subtilisin fold, and the covalently bound inhibitor is linked to the enzyme through a serine residue. Thus, the structure of PSCP defines a novel family of serine-carboxyl proteinases (defined as MEROPS S53) with a unique catalytic triad consisting of Glu 80, Asp 84 and Ser 287.


  • Organizational Affiliation
    • Protein Structure Section, Macromolecular Crystallography Laboratory, National Cancer Institute at Frederick, Maryland 21702, USA. wlodawer@ncifcrf.gov

Macromolecule Content 

  • Total Structure Weight: 39.44 kDa 
  • Atom Count: 3,345 
  • Modeled Residue Count: 371 
  • Deposited Residue Count: 375 
  • Unique protein chains: 2

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
SERINE-CARBOXYL PROTEINASE372Pseudomonas sp.Mutation(s): 0 
EC: 3.4.23.37 (PDB Primary Data), 3.4.21.100 (UniProt)
UniProt
Find proteins for P42790 (Pseudomonas sp. (strain 101))
Explore P42790 
Go to UniProtKB:  P42790
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP42790
Sequence Annotations
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Reference Sequence
Find similar proteins by:  Sequence   |   3D Structure  
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
FRAGMENT OF TYROSTATINB [auth I]3N/AMutation(s): 0 

Small Molecules

Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
GOL

Query on GOL



Download:Ideal Coordinates CCD File
H [auth A],
I [auth A],
J [auth A],
K [auth A]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
ACT

Query on ACT



Download:Ideal Coordinates CCD File
D [auth A],
E [auth A],
F [auth A],
G [auth A]
ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
CA

Query on CA



Download:Ideal Coordinates CCD File
C [auth A]CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.00 Å
  • R-Value Free:  0.131 (Depositor) 
  • R-Value Work:  0.123 (Depositor), 0.123 (DCC) 
  • R-Value Observed: 0.099 (Depositor) 
Space Group: P 62
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 97.4α = 90
b = 97.4β = 90
c = 83.35γ = 120
Software Package:
Software NamePurpose
HKL-2000data collection
HKL-2000data reduction
SHELXL-97refinement
HKL-2000data scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2000-12-13
    Type: Initial release
  • Version 1.1: 2008-04-27
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Non-polymer description, Version format compliance
  • Version 1.3: 2017-10-04
    Changes: Advisory, Refinement description
  • Version 1.4: 2023-08-09
    Changes: Advisory, Data collection, Database references, Derived calculations, Refinement description
  • Version 1.5: 2024-11-13
    Changes: Structure summary