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- PDB-7r27: Crystal structure of the L. plantarum D-alanine ligase DltA -

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Basic information

Entry
Database: PDB / ID: 7r27
TitleCrystal structure of the L. plantarum D-alanine ligase DltA
ComponentsD-alanine--D-alanyl carrier protein ligase
KeywordsCYTOSOLIC PROTEIN / D-alanine ligase / D-alanylation / AMP intermediate / teichoic acids
Function / homology
Function and homology information


D-alanine-[D-alanyl-carrier protein] ligase / D-alanine [D-alanyl carrier protein] ligase activity / lipoteichoic acid biosynthetic process / ATP binding / cytoplasm
Similarity search - Function
D-alanine--D-alanyl carrier protein ligase / D-alanine:D-alanyl carrier protein ligase-like / Amino acid adenylation domain / ANL, N-terminal domain / AMP-binding enzyme, C-terminal domain / AMP-binding enzyme C-terminal domain / AMP-binding, conserved site / Putative AMP-binding domain signature. / AMP-dependent synthetase/ligase / AMP-binding enzyme, C-terminal domain superfamily / AMP-binding enzyme
Similarity search - Domain/homology
ADENOSINE MONOPHOSPHATE / D-ALANINE / D-alanine--D-alanyl carrier protein ligase
Similarity search - Component
Biological speciesLactiplantibacillus plantarum subsp. plantarum NC8 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.01 Å
AuthorsNikolopoulos, N. / Ravaud, S. / Simorre, J.P. / Grangeasse, C.
Funding support France, 1items
OrganizationGrant numberCountry
Agence Nationale de la Recherche (ANR)18-CE15-0011-03 France
CitationJournal: Sci Rep / Year: 2022
Title: DltC acts as an interaction hub for AcpS, DltA and DltB in the teichoic acid D-alanylation pathway of Lactiplantibacillus plantarum.
Authors: Nikolopoulos, N. / Matos, R.C. / Courtin, P. / Ayala, I. / Akherraz, H. / Simorre, J.P. / Chapot-Chartier, M.P. / Leulier, F. / Ravaud, S. / Grangeasse, C.
History
DepositionFeb 4, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 3, 2022Provider: repository / Type: Initial release
Revision 1.1Aug 10, 2022Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.2Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: D-alanine--D-alanyl carrier protein ligase
B: D-alanine--D-alanyl carrier protein ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)113,1566
Polymers112,2832
Non-polymers8734
Water9,188510
1
A: D-alanine--D-alanyl carrier protein ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,5783
Polymers56,1421
Non-polymers4362
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: D-alanine--D-alanyl carrier protein ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,5783
Polymers56,1421
Non-polymers4362
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)68.522, 53.573, 102.072
Angle α, β, γ (deg.)90.000, 96.780, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein D-alanine--D-alanyl carrier protein ligase / DCL / D-alanine--poly(phosphoribitol) ligase subunit 1 / D-alanine-activating enzyme / DAE


Mass: 56141.562 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lactiplantibacillus plantarum subsp. plantarum NC8 (bacteria)
Gene: dltA, AYO51_00800 / Production host: Escherichia coli (E. coli)
References: UniProt: A0A151G8K4, D-alanine-[D-alanyl-carrier protein] ligase
#2: Chemical ChemComp-DAL / D-ALANINE


Type: D-peptide linking / Mass: 89.093 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H7NO2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-AMP / ADENOSINE MONOPHOSPHATE


Mass: 347.221 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H14N5O7P / Feature type: SUBJECT OF INVESTIGATION / Comment: AMP*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 510 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: PEG3350, KCl

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.97856 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 14, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97856 Å / Relative weight: 1
ReflectionResolution: 2.01→47.36 Å / Num. obs: 49012 / % possible obs: 99.4 % / Redundancy: 4.4 % / Rmerge(I) obs: 0.1713 / Net I/σ(I): 7.2
Reflection shellResolution: 2.01→2.06 Å / Rmerge(I) obs: 1.452 / Mean I/σ(I) obs: 0.9 / Num. unique obs: 3478

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Processing

Software
NameVersionClassification
PHENIX1.20_4459refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
Aimlessdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3DHV

3dhv


Resolution: 2.01→47.36 Å / SU ML: 0.29 / Cross valid method: THROUGHOUT / σ(F): 0 / Phase error: 31.02 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.266 1806 4.08 %
Rwork0.2092 42477 -
obs0.2115 44283 89.93 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 71.56 Å2 / Biso mean: 31.2965 Å2 / Biso min: 15.23 Å2
Refinement stepCycle: final / Resolution: 2.01→47.36 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6076 0 54 510 6640
Biso mean--46.18 33.83 -
Num. residues----792
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 13

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.01-2.070.39681190.31352692281174
2.07-2.130.31151250.28812890301580
2.13-2.20.35481260.25832961308783
2.2-2.270.33241310.25043113324486
2.27-2.360.2651320.25143197332988
2.36-2.470.33731380.24913203334189
2.47-2.60.3481420.25213262340491
2.6-2.770.28881410.2383397353893
2.77-2.980.29261450.25493444358994
2.98-3.280.33281460.23673445359195
3.28-3.750.23721500.18453557370798
3.75-4.730.18841520.14973610376298
4.73-47.360.20691590.16183706386598

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