1NYC | pdb_00001nyc

Staphostatins resemble lipocalins, not cystatins in fold.

• PDB DOI: https://doi.org/10.2210/pdb1NYC/pdb

• Classification: HYDROLASE INHIBITOR
• Organism(s): Staphylococcus aureus subsp. aureus MW2
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2003-02-12 Released: 2003-09-30 
• Deposition Author(s): Rzychon, M., Filipek, R., Sabat, A., Kosowska, K., Dubin, A., Potempa, J., Bochtler, M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.40 Å
• R-Value Free: 
  0.226 (Depositor), 0.231 (DCC) 
• R-Value Work: 
  0.201 (Depositor), 0.208 (DCC) 
• R-Value Observed: 
  0.202 (Depositor) 

Literature

Staphostatins resemble lipocalins, not cystatins in fold.

Rzychon, M., Filipek, R., Sabat, A., Kosowska, K., Dubin, A., Potempa, J., Bochtler, M.

(2003) Protein Sci 12: 2252-2256

• PubMed: 14500882 
• DOI: https://doi.org/10.1110/ps.03247703
• Primary Citation Related Structures: 
  1NYC


• PubMed Abstract: 
  

  Staphostatins are the endogenous inhibitors of the major secreted cysteine proteases of Staphylococcus aureus, the staphopains. Here, we present the 1.4 A crystal structure of staphostatin B and show that the fold can be described as a fully closed, highly sheared eight-stranded beta-barrel. Thus, staphostatin B is related to beta-barrel domains that are involved in the inhibition or regulation of proteases of various catalytic types and to the superfamily of lipocalins/cytosolic fatty acid binding proteins. Unexpectedly for a cysteine protease inhibitor, staphostatin B is not significantly similar to cystatins.

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Organizational Affiliation: 
• International Institute of Molecular and Cell Biology, 02109 Warsaw, Poland.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly 2  

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

Biological assembly 2 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 26.32 kDa 
• Atom Count: 2,111 
• Modeled Residue Count: 222 
• Deposited Residue Count: 222 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
cysteine protease inhibitor	A, B	111	Staphylococcus aureus subsp. aureus MW2	Mutation(s): 0  Gene Names: staphostatin B (sspC)
UniProt
Find proteins for Q7A189 (Staphylococcus aureus (strain MW2)) Explore Q7A189  Go to UniProtKB:  Q7A189

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	E [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
CL	C [auth A], D [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.40 Å
• R-Value Free:  0.226 (Depositor), 0.231 (DCC) 
• R-Value Work:  0.201 (Depositor), 0.208 (DCC) 
• R-Value Observed: 0.202 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 34.196	α = 90
b = 77.049	β = 90
c = 101.271	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
DENZO	data reduction
SCALEPACK	data scaling
MLPHARE	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2003-09-30 
Deposition Author(s): Rzychon, M., Filipek, R., Sabat, A., Kosowska, K., Dubin, A., Potempa, J., Bochtler, M.

Revision History  

• Version 1.0: 2003-09-30
  Type: Initial release
  
• Version 1.1: 2008-04-29
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Source and taxonomy, Version format compliance
• Version 1.3: 2024-02-14
  Changes: Data collection, Database references, Derived calculations