1GA1

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.40 Å
  • R-Value Free: 0.136 
  • R-Value Work: 0.113 
  • R-Value Observed: 0.108 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Practical experience with the use of halides for phasing macromolecular structures: a powerful tool for structural genomics.

Dauter, Z.Li, M.Wlodawer, A.

(2001) Acta Crystallogr D Biol Crystallogr 57: 239-249

  • DOI: 10.1107/s0907444900015249
  • Primary Citation of Related Structures:  
    1GA1

  • PubMed Abstract: 
  • The crystal structure of pepstatin-insensitive carboxyl proteinase (PCP) from Pseudomonas sp. 101, an enzyme with no overall sequence similarity to any other proteinases of known structure, was solved using crystals soaked in sodium bromide solution and then cryocooled ...

    The crystal structure of pepstatin-insensitive carboxyl proteinase (PCP) from Pseudomonas sp. 101, an enzyme with no overall sequence similarity to any other proteinases of known structure, was solved using crystals soaked in sodium bromide solution and then cryocooled. A data set collected at the bromine peak absorption wavelength was sufficient for calculation of an excellent map and the entire process of phasing and tracing the maps required almost no direct human intervention. The process of structure solution using single-wavelength data was compared with three-wavelength multiwavelength anomalous diffraction (MAD); although the latter resulted in slightly better maps, the use of this much more labor-intensive approach did not significantly improve the ability to solve the structure. The successful phasing approaches are compared with several less successful attempts utilizing other crystal forms of the enzyme and the practical aspects of the use of bromine as a heavy-atom derivative are discussed. In conclusion, the use of halides with single-wavelength diffraction data fulfills the requirements of being a first-choice method of high-throughput structure solution for the emerging field of structural genomics.


    Related Citations: 
    • 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

    Organizational Affiliation

    Synchrotron Radiation Research Section, Macromolecular Crystallography Laboratory, Program in Structural Biology, National Cancer Institute and NSLS, Brookhaven National Laboratory, Building 725A-X9, Upton, NY 11973, USA. dauter@bnl.gov



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
SERINE-CARBOXYL PROTEINASEA372Pseudomonas 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
Protein Feature View
Expand
  • Reference Sequence
  • Find similar proteins by:  Sequence   |   Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
FRAGMENT OF IODOTYROSTATINB [auth I]3N/AMutation(s): 0 
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GOL
Query on GOL

Download Ideal Coordinates CCD File 
E [auth A]GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
CA
Query on CA

Download Ideal Coordinates CCD File 
C [auth A]CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
CL
Query on CL

Download Ideal Coordinates CCD File 
D [auth A]CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
PHI
Query on PHI
B [auth I]L-PEPTIDE LINKINGC9 H10 I N O2PHE
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.40 Å
  • R-Value Free: 0.136 
  • R-Value Work: 0.113 
  • R-Value Observed: 0.108 
  • Space Group: P 62
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 97.19α = 90
b = 97.19β = 90
c = 83.37γ = 120
Software Package:
Software NamePurpose
HKL-2000data collection
HKL-2000data reduction
SHELXDphasing
SHARPphasing
DMmodel building
WARPmodel building
SHELXL-97refinement
HKL-2000data scaling
DMphasing
ARP/wARPmodel building

Structure Validation

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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