1JWQ | pdb_00001jwq

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.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.80 Å
R-Value Free:
0.206 (Depositor), 0.206 (DCC)
R-Value Work:
0.176 (Depositor), 0.177 (DCC)

wwPDB Validation 3D Report Full Report

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This is version 1.4 of the entry. See complete history.

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.

Macromolecule Content

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

Macromolecules

Find similar proteins by:

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
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q9LCR3
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ZN Query on ZN Download:Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.80 Å
R-Value Free: 0.206 (Depositor), 0.206 (DCC)
R-Value Work: 0.176 (Depositor), 0.177 (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

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Entry History

Deposition Data

Released Date: 2003-11-18

Deposition Author(s):

Revision History (Full details and data files)

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

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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.