1JWQ

Structure of the catalytic domain of CwlV, N-acetylmuramoyl-L-alanine amidase from Bacillus(Paenibacillus) polymyxa var.colistinus

• PDB DOI: https://doi.org/10.2210/pdb1JWQ/pdb

• Classification: HYDROLASE
• Organism(s): Paenibacillus polymyxa
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2001-09-05 Released: 2003-11-18 
• Deposition Author(s): Yamane, T., Koyama, Y., Nojiri, Y., Hikage, T., Akita, M., Suzuki, A., Shirai, T., Ise, F., Shida, T., Sekiguchi, J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 
  0.206 (Depositor), 0.210 (DCC) 
• R-Value Work: 
  0.176 (Depositor), 0.180 (DCC) 

Literature

The Structure of the catalytic domain of N-acetylmuramoyl-L-alanine amidase, a cell wall hydrolase from Bacillus polymyxa var.colistinus and its resemblance to the structure of carboxypeptidases

Yamane, T., Koyama, Y., Nojiri, Y., Hikage, T., Akita, M., Suzuki, A., Shirai, T., Ise, F., Shida, T., Sekiguchi, J.

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 19.77 kDa 
• Atom Count: 1,593 
• Modelled Residue Count: 179 
• Deposited Residue Count: 179 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
N-ACETYLMURAMOYL-L-ALANINE AMIDASE CwlV	A	179	Paenibacillus polymyxa	Mutation(s): 0  EC: 3.5.1.28
UniProt
Find proteins for Q9LCR3 (Paenibacillus polymyxa) Explore Q9LCR3  Go to UniProtKB:  Q9LCR3

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ZN	B [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free:  0.206 (Depositor), 0.210 (DCC) 
• R-Value Work:  0.176 (Depositor), 0.180 (DCC) 

Space Group: P 6₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 66.5	α = 90
b = 66.5	β = 90
c = 88.34	γ = 120

Software Package:

Software Name	Purpose
MOSFLM	data reduction
SCALA	data scaling
MLPHARE	phasing
CNS	refinement
CCP4	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2003-11-18 
Deposition Author(s): Yamane, T., Koyama, Y., Nojiri, Y., Hikage, T., Akita, M., Suzuki, A., Shirai, T., Ise, F., Shida, T., Sekiguchi, J.

Revision History  

• Version 1.0: 2003-11-18
  Type: Initial release
  
• Version 1.1: 2008-04-27
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2022-12-21
  Changes: Database references, Derived calculations
• Version 1.4: 2024-05-29
  Changes: Data collection