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)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.70 Å
R-Value Free:
0.262 (Depositor), 0.263 (DCC)
R-Value Work:
0.189 (Depositor), 0.190 (DCC)
R-Value Observed:
0.193 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 7Y6M

This is version 1.1 of the entry. See complete history.

Literature

Intracellular Subtilisin from Bacillus sp.

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

To be published.

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

Find similar proteins by:

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
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0A7H0M7J5
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PEG Query on PEG Download:Ideal Coordinates CCD File SDF format, chain H [auth D] SDF format, chain E [auth C] MOL2 format, chain H [auth D] MOL2 format, chain E [auth C] mmCIF format, chain H [auth D] mmCIF format, chain E [auth C]	E [auth C], H [auth D]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain E [auth C] Focus chain H [auth D] Interactions & Density Focus chain E [auth C] Focus chain H [auth D]
CA (Subject of Investigation/LOI) Query on CA Download:Ideal Coordinates CCD File SDF format, chain F [auth C] SDF format, chain J [auth D] SDF format, chain I [auth D] SDF format, chain G [auth C] MOL2 format, chain F [auth C] MOL2 format, chain J [auth D] MOL2 format, chain I [auth D] MOL2 format, chain G [auth C] mmCIF format, chain F [auth C] mmCIF format, chain J [auth D] mmCIF format, chain I [auth D] mmCIF format, chain G [auth C]	F [auth C], G [auth C], I [auth D], J [auth D]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain F [auth C] Focus chain G [auth C] Focus chain I [auth D] Focus chain J [auth D] Interactions & Density Focus chain F [auth C] Focus chain G [auth C] Focus chain I [auth D] Focus chain J [auth D]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.70 Å
R-Value Free: 0.262 (Depositor), 0.263 (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

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View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2022-07-20

Deposition Author(s):

This entry supersedes: 7XAS

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

Revision History (Full details and data files)

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

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.