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: 1.4 Å
  • R-Value Free: 0.136 
  • R-Value Work: 0.113 

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.,Sect.D 57: 239-249


  • 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 ...

    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.Mol.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: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
SERINE-CARBOXYL PROTEINASE
A
372Pseudomonas sp. (strain 101)Gene Names: pcp
EC: 3.4.21.100
Find proteins for P42790 (Pseudomonas sp. (strain 101))
Go to UniProtKB:  P42790
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
FRAGMENT OF IODOTYROSTATIN
I
3N/AN/A
Protein Feature View is not available: No corresponding UniProt sequence found.
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CL
Query on CL

Download SDF File 
Download CCD File 
A
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
GOL
Query on GOL

Download SDF File 
Download CCD File 
A
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
CA
Query on CA

Download SDF File 
Download CCD File 
A
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  2 Unique
IDChainsTypeFormula2D DiagramParent
UNK
Query on UNK
I
L-PEPTIDE LINKINGC4 H9 N O2

--

PHI
Query on PHI
I
L-PEPTIDE LINKINGC9 H10 I N O2PHE
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.4 Å
  • R-Value Free: 0.136 
  • R-Value Work: 0.113 
  • Space Group: P 62
Unit Cell:
Length (Å)Angle (°)
a = 97.190α = 90.00
b = 97.190β = 90.00
c = 83.370γ = 120.00
Software Package:
Software NamePurpose
DMphasing
ARP/wARPmodel building
WARPmodel building
HKL-2000data reduction
HKL-2000data scaling
SHELXDphasing
SHELXL-97refinement
DMmodel building
SHARPphasing
HKL-2000data collection

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2000-12-13
    Type: Initial release
  • Version 1.1: 2008-04-27
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Non-polymer description, Version format compliance