9LNF | pdb_00009lnf

Crystal structure of SpoIVB_101-426-S378A

• PDB DOI: https://doi.org/10.2210/pdb9LNF/pdb

• Classification: HYDROLASE
• Organism(s): Bacillus subtilis subsp. subtilis str. 168
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2025-01-21 Released: 2025-08-13 
• Deposition Author(s): Jiang, L.G., Zhu, J., Huang, M.D.
• Funding Organization(s): National Natural Science Foundation of China (NSFC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.49 Å
• R-Value Free: 
  0.287 (Depositor), 0.292 (DCC) 
• R-Value Work: 
  0.236 (Depositor), 0.246 (DCC) 
• R-Value Observed: 
  0.238 (Depositor) 

Starting Model: in silico

Literature

Crystal structure of SpoIVB_101-426-S378A

Jiang, L.G., Zhu, J., Huang, M.D.

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 35.58 kDa 
• Atom Count: 2,509 
• Modeled Residue Count: 330 
• Deposited Residue Count: 330 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
SpoIVB peptidase 42 kDa isoform	A	330	Bacillus subtilis subsp. subtilis str. 168	Mutation(s): 0  Gene Names: spoIVB, BSU24230 EC: 3.4.21.116
UniProt
Find proteins for P17896 (Bacillus subtilis (strain 168)) Explore P17896  Go to UniProtKB:  P17896

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.49 Å
• R-Value Free:  0.287 (Depositor), 0.292 (DCC) 
• R-Value Work:  0.236 (Depositor), 0.246 (DCC) 
• R-Value Observed: 0.238 (Depositor) 

Space Group: P 6₂

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 72.19	α = 90
b = 72.19	β = 90
c = 108.44	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling
MOLREP	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-08-13 
Deposition Author(s): Jiang, L.G., Zhu, J., Huang, M.D.

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Funding Organization	Location	Grant Number
National Natural Science Foundation of China (NSFC)	China	32370990

Revision History  

• Version 1.0: 2025-08-13
  Type: Initial release