1GA4 | pdb_00001ga4

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

• PDB DOI: https://doi.org/10.2210/pdb1GA4/pdb

• Classification: HYDROLASE/HYDROLASE INHIBITOR
• Organism(s): Pseudomonas sp.
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2000-11-29 Released: 2000-12-13 
• Deposition Author(s): Wlodawer, A., Li, M., Dauter, Z., Gustchina, A., Uchida, K.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.40 Å
• R-Value Free: 
  0.155 (Depositor) 
• R-Value Work: 
  0.118 (Depositor), 0.117 (DCC) 
• R-Value Observed: 
  0.103 (Depositor) 

Starting Model: experimental

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

• PubMed: 11323721 
• 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.

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Organizational Affiliation: 
• Protein Structure Section, Macromolecular Crystallography Laboratory, National Cancer Institute at Frederick, Maryland 21702, USA. [e-mail]

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 39.1 kDa 
• Atom Count: 3,249 
• Modeled Residue Count: 372 
• Deposited Residue Count: 375 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
SERINE-CARBOXYL PROTEINASE	A	372	Pseudomonas 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 ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
PSEUDOIODOTYROSTATIN	B [auth I]	3	N/A	Mutation(s): 0

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GOL	D [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
CA	C [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Modified Residues  2 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
PHI	B [auth I]	L-PEPTIDE LINKING	C9 H10 I N O2		PHE
TYB	B [auth I]	L-PEPTIDE LINKING	C9 H11 N O2		TYR

Biologically Interesting Molecules (External Reference) 

1 Unique

Entity ID: 2
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_000754	B [auth I]	PSEUDO-IODOTYROSTATIN	Peptide-like / Inhibitor

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.40 Å
• R-Value Free:  0.155 (Depositor) 
• R-Value Work:  0.118 (Depositor), 0.117 (DCC) 
• R-Value Observed: 0.103 (Depositor) 

Space Group: P 6₂

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 97.63	α = 90
b = 97.63	β = 90
c = 83.3	γ = 120

Software Package:

Software Name	Purpose
HKL-2000	data collection
HKL-2000	data reduction
SHELXL-97	refinement
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2000-12-13 
Deposition Author(s): Wlodawer, A., Li, M., Dauter, Z., Gustchina, A., Uchida, K.

Revision History  

• 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: Atomic model, Database references, Derived calculations, Non-polymer description, Structure summary, Version format compliance
• Version 1.3: 2012-12-12
  Changes: Other
• Version 1.4: 2017-10-04
  Changes: Advisory, Refinement description
• Version 1.5: 2023-08-09
  Changes: Advisory, Data collection, Database references, Derived calculations, Refinement description