3K3P

Crystal Structure of the Apo Form of D-Alanine:D-Alanine Ligase (DDl) from Streptococcus mutans

PDB DOI: https://doi.org/10.2210/pdb3K3P/pdb

Classification: LIGASE
Organism(s): Streptococcus mutans
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2009-10-03 Released: 2010-09-15
Deposition Author(s): Lu, Y.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.23 Å
R-Value Free: 0.248
R-Value Work: 0.196
R-Value Observed: 0.199

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

This is version 1.3 of the entry. See complete history.

Literature

Crystal structure of the Apo form of D-Alanine:D-Alanine ligase (DDl) from Streptococcus mutans.

Lu, Y., Xu, H., Zhao, X.

(2010) Protein Pept Lett 17: 1053-1057

PubMed: 20522004 Search on PubMed
DOI: https://doi.org/10.2174/092986610791498858
Primary Citation of Related Structures:
3K3P

PubMed Abstract:
D-Alanine:D-Alanine ligase (DDl) catalyzes the formation of D-Alanine:D-Alanine dipeptide and is an essential enzyme in bacterial cell wall biosynthesis.. This enzyme does not have a human ortholog, making it an attractive target for developing new antibiotic drugs. We determined the crystal structure at 2.23 A resolution of DDl from Streptococcus mutans (SmDDl), the principal aetiological agent of human dental caries. This structure reveals that SmDDl is a dimer and has a disordered omega-loop region.

Organizational Affiliation

West China Hospital Nanomedicine Laboratory, Center for Regenerative Medicine and Institute for Nanobiomedical Technology and Membrane Biology, West China Hospital Sichuan University, Chengdu 610065, Sichuan, China.

Macromolecule Content

Total Structure Weight: 84.85 kDa
Atom Count: 5,080
Modelled Residue Count: 635
Deposited Residue Count: 766
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
D-alanine--D-alanine ligase	A, B	383	Streptococcus mutans	Mutation(s): 0 Gene Names: ddl EC: 6.3.2.4
UniProt
Find proteins for P95803 (Streptococcus mutans serotype c (strain ATCC 700610 / UA159)) Explore P95803 Go to UniProtKB: P95803
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P95803
Sequence Annotations Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.23 Å
R-Value Free: 0.248
R-Value Work: 0.196
R-Value Observed: 0.199
Space Group: P 3₂

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 79.502	α = 90
b = 79.502	β = 90
c = 109.4	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
CrysalisPro	data reduction
SCALA	data scaling
MOLREP	phasing

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Released Date: 2010-09-15

Deposition Author(s):

Lu, Y.

Revision History (Full details and data files)

Version 1.0: 2010-09-15
Type: Initial release
Version 1.1: 2011-07-13
Changes: Version format compliance
Version 1.2: 2019-10-16
Changes: Advisory, Data collection, Database references
Version 1.3: 2023-11-01
Changes: Advisory, Data collection, Database references, Refinement description