7Y6M | pdb_00007y6m

Intracellular Subtilisin from Bacillus sp.

• PDB DOI: https://doi.org/10.2210/pdb7Y6M/pdb
• Entry: 7Y6M supersedes: 7XAS

• Classification: HYDROLASE
• Organism(s): Bacillus sp. (in: firmicutes)
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2022-06-21 Released: 2022-07-20 
• Deposition Author(s): Hussin, N., Jamaluddin, H., Jonet, M.A.
• Funding Organization(s): The University Grants Committee, Research Grants Council (RGC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.70 Å
• R-Value Free: 
  0.262 (Depositor), 0.260 (DCC) 
• R-Value Work: 
  0.189 (Depositor), 0.190 (DCC) 
• R-Value Observed: 
  0.193 (Depositor) 

Starting Model: experimental

Literature

Intracellular Subtilisin from Bacillus sp.

Hussin, N., Jamaluddin, H., Jonet, M.A.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Hetero 4-mer - A2B2 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 4-mer - A2B1C1 

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

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 147.37 kDa 
• Atom Count: 4,553 
• Modeled Residue Count: 594 
• Deposited Residue Count: 1,372 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Intracellular serine protease	A [auth C], B [auth D], C [auth A], D [auth B]	343	Bacillus sp. (in: firmicutes)	Mutation(s): 0  Gene Names: intracellular serine protease EC: 3.4.21
UniProt
Find proteins for A0A7H0M7J5 (Bacillus pumilus) Explore A0A7H0M7J5  Go to UniProtKB:  A0A7H0M7J5

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PEG	E [auth C], H [auth D]	DI(HYDROXYETHYL)ETHER C4 H10 O3 MTHSVFCYNBDYFN-UHFFFAOYSA-N
CA (Subject of Investigation/LOI)	F [auth C], G [auth C], I [auth D], J [auth D]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.70 Å
• R-Value Free:  0.262 (Depositor), 0.260 (DCC) 
• R-Value Work:  0.189 (Depositor), 0.190 (DCC) 
• R-Value Observed: 0.193 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 64.057	α = 90
b = 78.778	β = 90
c = 113.19	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
PDB_EXTRACT	data extraction
HKL-3000	data reduction
HKL-3000	phasing
HKL-3000	data scaling

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2022-07-20 
Deposition Author(s): Hussin, N., Jamaluddin, H., Jonet, M.A.
• This entry supersedes: 7XAS

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Funding Organization	Location	Grant Number
The University Grants Committee, Research Grants Council (RGC)	Malaysia	--

Revision History  

• Version 1.0: 2022-07-20
  Type: Initial release
  
• Version 1.1: 2023-11-29
  Changes: Data collection, Refinement description