4HX3

Crystal structure of Streptomyces caespitosus sermetstatin in complex with S. caespitosus snapalysin

• PDB DOI: https://doi.org/10.2210/pdb4HX3/pdb

• Classification: Hydrolase/Hydrolase Inhibitor
• Organism(s): Streptomyces caespitosus
• Expression System: Escherichia coli BL21(DE3), Escherichia coli
• Mutation(s): No 


• Deposited: 2012-11-09 Released: 2012-12-05 
• Deposition Author(s): Trillo-Muyo, S., Martinez-Rodriguez, S., Arolas, J.L., Gomis-Ruth, F.X.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.70 Å
• R-Value Free: 0.242 
• R-Value Work: 0.195 
• R-Value Observed: 0.196 

Literature

Mechanism of action of a Janus-faced single-domain protein inhibitor simultaneously targeting two peptidase classes

Trillo-Muyo, S., Martinez-Rodriguez, S., Arolas, J.L., Gomis-Ruth, F.X.

(2013) Chem Sci 4: 791-797

• DOI: https://doi.org/10.1039/C2SC21712K

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Hetero 4-mer - A2B2 

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

Biological Assembly 2  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Hetero 4-mer - A2B2 

Biological assembly 2 assigned by authors and generated by PISA (software)

Biological Assembly 3  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Hetero 4-mer - A2B2 

Biological assembly 3 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 159.55 kDa 
• Atom Count: 11,334 
• Modelled Residue Count: 1,466 
• Deposited Residue Count: 1,488 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Extracellular small neutral protease	A, C, E, G, I, K	134	Streptomyces caespitosus	Mutation(s): 0  Gene Names: snpA EC: 3.4.24.77
UniProt
Find proteins for P56406 (Streptomyces caespitosus) Explore P56406  Go to UniProtKB:  P56406

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Neutral proteinase inhibitor ScNPI	B, D, F, H, J, L	114	Streptomyces caespitosus	Mutation(s): 0  Gene Names: ScNPI
UniProt
Find proteins for Q9FDS0 (Streptomyces caespitosus) Explore Q9FDS0  Go to UniProtKB:  Q9FDS0

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GOL	O [auth D], S [auth J]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
ZN	M [auth A], N [auth C], P [auth E], Q [auth G], R [auth I], T [auth K]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.70 Å
• R-Value Free: 0.242 
• R-Value Work: 0.195 
• R-Value Observed: 0.196 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 116.54	α = 90
b = 121.81	β = 90
c = 130.67	γ = 90

Software Package:

Software Name	Purpose
ProDC	data collection
PHASER	phasing
BUSTER	refinement
XDS	data reduction
SCALA	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2012-12-05 
Deposition Author(s): Trillo-Muyo, S., Martinez-Rodriguez, S., Arolas, J.L., Gomis-Ruth, F.X.

Revision History  

• Version 1.0: 2012-12-05
  Type: Initial release
  
• Version 1.1: 2013-02-20
  Changes: Database references
• Version 1.2: 2013-02-27
  Changes: Database references
• Version 1.3: 2017-11-15
  Changes: Refinement description
• Version 1.4: 2023-09-20
  Changes: Data collection, Database references, Derived calculations, Refinement description