4HX2 | pdb_00004hx2

Crystal structure of Streptomyces caespitosus sermetstatin in complex with Bacillus licheniformis subtilisin

• PDB DOI: https://doi.org/10.2210/pdb4HX2/pdb

• Classification: Hydrolase/Hydrolase Inhibitor
• Organism(s): Bacillus licheniformis, Streptomyces caespitosus
• Expression System: 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: 2.25 Å
• R-Value Free: 
  0.217 (Depositor), 0.220 (DCC) 
• R-Value Work: 
  0.177 (Depositor), 0.180 (DCC) 
• R-Value Observed: 
  0.177 (Depositor) 

Starting Models: experimental

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.

Macromolecule Content

• Total Structure Weight: 79.69 kDa 
• Atom Count: 5,900 
• Modelled Residue Count: 772 
• Deposited Residue Count: 776 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
KerA	A, C	274	Bacillus licheniformis	Mutation(s): 0  EC: 3.4.21.62
UniProt
Find proteins for Q9FDF2 (Bacillus licheniformis) Explore Q9FDF2  Go to UniProtKB:  Q9FDF2

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Neutral proteinase inhibitor ScNPI	B, D	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 10 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
1AX	I [auth A]	(2R,2'R)-3,3'-oxydipropane-1,2-diol C6 H14 O5 GPLRAVKSCUXZTP-PHDIDXHHSA-N
CAC	P [auth B]	CACODYLATE ION C2 H6 As O2 OGGXGZAMXPVRFZ-UHFFFAOYSA-M
PO4	J [auth A]	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K
GOL	K [auth A], T [auth C]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
ZN	G [auth A], M [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
IPA	L [auth A], U [auth C], V [auth D]	ISOPROPYL ALCOHOL C3 H8 O KFZMGEQAYNKOFK-UHFFFAOYSA-N
ACT	S [auth C]	ACETATE ION C2 H3 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-M
CA	E [auth A], F [auth A], Q [auth C], R [auth C]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N
K	N [auth B], O [auth B]	POTASSIUM ION K NPYPAHLBTDXSSS-UHFFFAOYSA-N
CL	H [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.25 Å
• R-Value Free:  0.217 (Depositor), 0.220 (DCC) 
• R-Value Work:  0.177 (Depositor), 0.180 (DCC) 
• R-Value Observed: 0.177 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 183.969	α = 90
b = 83.624	β = 110.78
c = 77.617	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
• Version 1.5: 2024-11-06
  Changes: Structure summary