2Z3B | pdb_00002z3b

Crystal Structure of Bacillus Subtilis CodW, a non-canonical HslV-like peptidase with an impaired catalytic apparatus

• PDB DOI: https://doi.org/10.2210/pdb2Z3B/pdb

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


• Deposited: 2007-06-03 Released: 2008-03-25 
• Deposition Author(s): Rho, S.H., Park, H.H., Kang, G.B., Lim, Y.J., Kang, M.S., Lim, B.K., Seong, I.S., Chung, C.H., Wang, J., Eom, S.H.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 
  0.265 (Depositor), 0.245 (DCC) 
• R-Value Work: 
  0.226 (Depositor), 0.206 (DCC) 
• R-Value Observed: 
  0.228 (Depositor) 

Literature

Crystal structure of Bacillus subtilis CodW, a noncanonical HslV-like peptidase with an impaired catalytic apparatus

Rho, S.H., Park, H.H., Kang, G.B., Im, Y.J., Kang, M.S., Lim, B.K., Seong, I.S., Seol, J., Chung, C.H., Wang, J., Eom, S.H.

(2007) Proteins 71: 1020-1026

• PubMed: 17979190 
• DOI: https://doi.org/10.1002/prot.21758
• Primary Citation Related Structures: 
  2Z3A, 2Z3B

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Organizational Affiliation: 
• Department of Life Science, Cell Dynamics Research Center, Gwangju Institute of Science and Technology, Gwangju 500-712, Korea.

Biological Assembly 1  

Global Symmetry: Dihedral - D6  (Explore in 3D)
Global Stoichiometry: Homo 12-mer - A12 

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

Biological Assembly 2  

Global Symmetry: Dihedral - D6  (Explore in 3D)
Global Stoichiometry: Homo 12-mer - A12 

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

Macromolecule Content 

• Total Structure Weight: 232.74 kDa 
• Atom Count: 16,571 
• Modeled Residue Count: 2,160 
• Deposited Residue Count: 2,160 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
ATP-dependent protease hslV	A, B, C, D, E, F, G, H, I, J, K, L	180	Bacillus subtilis	Mutation(s): 0  Gene Names: CODW EC: 3.4.25 (PDB Primary Data), 3.4.21 (UniProt)
UniProt
Find proteins for P39070 (Bacillus subtilis (strain 168)) Explore P39070  Go to UniProtKB:  P39070

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NA	M [auth A], N [auth B], O [auth C], P [auth D], Q [auth E], R [auth F], S [auth G], T [auth H], U [auth I], V [auth J], W [auth K], X [auth L]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free:  0.265 (Depositor), 0.245 (DCC) 
• R-Value Work:  0.226 (Depositor), 0.206 (DCC) 
• R-Value Observed: 0.228 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 185.05	α = 90
b = 106.8	β = 112
c = 152.7	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
REFMAC	refinement
DENZO	data reduction
SCALEPACK	data scaling
MOSFLM	data reduction
SCALA	data scaling
CNS	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2008-03-25 
Deposition Author(s): Rho, S.H., Park, H.H., Kang, G.B., Lim, Y.J., Kang, M.S., Lim, B.K., Seong, I.S., Chung, C.H., Wang, J., Eom, S.H.

Revision History  

• Version 1.0: 2008-03-25
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2017-10-11
  Changes: Refinement description
• Version 1.3: 2024-03-13
  Changes: Data collection, Database references, Derived calculations, Refinement description