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- PDB-7r49: Crystal structure of the L. plantarum acyl carrier protein syntha... -

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Basic information

Entry
Database: PDB / ID: 7r49
TitleCrystal structure of the L. plantarum acyl carrier protein synthase (AcpS)in complex with D-alanyl carrier protein (DltC1)
Components
  • D-alanyl carrier protein 1
  • Holo-[acyl-carrier-protein] synthase
KeywordsCYTOSOLIC PROTEIN / acyl carrier protein synthase / D-alanyl carrier protein / Complex / D-alanylation / teichoic acids
Function / homology
Function and homology information


D-alanyl carrier activity / lipoteichoic acid biosynthetic process / holo-[acyl-carrier-protein] synthase / holo-[acyl-carrier-protein] synthase activity / cell wall organization / fatty acid biosynthetic process / magnesium ion binding / cytoplasm
Similarity search - Function
D-alanyl carrier protein / Holo-[acyl carrier protein] synthase / Phosphopantetheine-protein transferase domain / 4'-phosphopantetheinyl transferase domain / 4'-phosphopantetheinyl transferase domain superfamily / 4'-phosphopantetheinyl transferase superfamily / Phosphopantetheine attachment site / ACP-like superfamily / Carrier protein (CP) domain profile. / Phosphopantetheine binding ACP domain
Similarity search - Domain/homology
4'-PHOSPHOPANTETHEINE / D-alanyl carrier protein 1 / Holo-[acyl-carrier-protein] synthase
Similarity search - Component
Biological speciesLactiplantibacillus plantarum subsp. plantarum NC8 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.88 Å
AuthorsNikolopoulos, N. / Ravaud, S. / Simorre, J.P. / Grangeasse, C.
Funding support France, 1items
OrganizationGrant numberCountry
Agence Nationale de la Recherche (ANR)18-CE15-011-03 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 8, 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: Holo-[acyl-carrier-protein] synthase
H: D-alanyl carrier protein 1
B: Holo-[acyl-carrier-protein] synthase
E: D-alanyl carrier protein 1
C: Holo-[acyl-carrier-protein] synthase
F: D-alanyl carrier protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,0228
Polymers69,5416
Non-polymers4802
Water6,359353
1
A: Holo-[acyl-carrier-protein] synthase
H: D-alanyl carrier protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,5393
Polymers23,1802
Non-polymers3581
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1980 Å2
ΔGint-12 kcal/mol
Surface area10050 Å2
MethodPISA
2
B: Holo-[acyl-carrier-protein] synthase
E: D-alanyl carrier protein 1


Theoretical massNumber of molelcules
Total (without water)23,1802
Polymers23,1802
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1450 Å2
ΔGint-10 kcal/mol
Surface area10580 Å2
MethodPISA
3
C: Holo-[acyl-carrier-protein] synthase
F: D-alanyl carrier protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,3023
Polymers23,1802
Non-polymers1221
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1450 Å2
ΔGint-9 kcal/mol
Surface area9910 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.537, 94.888, 98.709
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Holo-[acyl-carrier-protein] synthase / Holo-ACP synthase / 4'-phosphopantetheinyl transferase AcpS


Mass: 13307.321 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lactiplantibacillus plantarum subsp. plantarum NC8 (bacteria)
Strain: ATCC BAA-793 / NCIMB 8826 / WCFS1 / Gene: acpS, lp_0522 / Production host: Escherichia coli (E. coli)
References: UniProt: Q88Z44, holo-[acyl-carrier-protein] synthase
#2: Protein D-alanyl carrier protein 1 / DCP 1 / D-alanine--poly(phosphoribitol) ligase subunit 2-1


Mass: 9873.019 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lactiplantibacillus plantarum subsp. plantarum NC8 (bacteria)
Strain: ATCC BAA-793 / NCIMB 8826 / WCFS1 / Gene: dltC1, lp_2017 / Production host: Escherichia coli (E. coli) / References: UniProt: Q88VM8
#3: Chemical ChemComp-PNS / 4'-PHOSPHOPANTETHEINE / Phosphopantetheine


Mass: 358.348 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H23N2O7PS / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER / Tris


Mass: 122.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 353 / 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

CrystalDensity Matthews: 2.3 Å3/Da / Density % sol: 46.44 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: PEG3350, Sodium Malonate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID30B / Wavelength: 0.9677 Å
DetectorType: DECTRIS EIGER X 4M / Detector: PIXEL / Date: Apr 7, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9677 Å / Relative weight: 1
ReflectionResolution: 1.88→43.79 Å / Num. obs: 52945 / % possible obs: 99.3 % / Redundancy: 13.4 % / Rpim(I) all: 0.063 / Net I/σ(I): 9.1
Reflection shellResolution: 1.88→1.92 Å / Mean I/σ(I) obs: 1.4 / Num. unique obs: 3096 / Rpim(I) all: 0.569

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Processing

Software
NameVersionClassification
PHENIX1.20_4459refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
XDSdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1F80

1f80


Resolution: 1.88→43.79 Å / SU ML: 0.3 / Cross valid method: THROUGHOUT / σ(F): 1.29 / Phase error: 29.27 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2625 2012 3.98 %
Rwork0.2157 48495 -
obs0.2176 50507 95.8 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 88.27 Å2 / Biso mean: 34.2159 Å2 / Biso min: 15.88 Å2
Refinement stepCycle: final / Resolution: 1.88→43.79 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4561 0 8 353 4922
Biso mean--29.91 36.17 -
Num. residues----591
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.88-1.930.5624830.50681874195753
1.93-1.980.32071430.339835763719100
1.98-2.040.30161530.25735753728100
2.04-2.110.31871480.230435843732100
2.11-2.180.27511430.235535553698100
2.18-2.270.42181270.38233210333790
2.27-2.370.32551450.23953558370399
2.37-2.50.25231420.226435613703100
2.5-2.660.29381570.209936123769100
2.66-2.860.24591470.214136273774100
2.86-3.150.26691550.216336043759100
3.15-3.60.25871520.197436413793100
3.6-4.540.21931490.173936873836100
4.54-43.790.21211680.176938313999100

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