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- PDB-8akh: Crystal structure of DltE from L. plantarum soaked with LTA -

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Basic information

Entry
Database: PDB / ID: 8akh
TitleCrystal structure of DltE from L. plantarum soaked with LTA
ComponentsBeta-lactamase family protein
KeywordsCELL CYCLE / carboxyesterase / D-alanylation / lipoteichoic acids
Function / homologyserine-type D-Ala-D-Ala carboxypeptidase / serine-type D-Ala-D-Ala carboxypeptidase activity / Beta-lactamase-related / Beta-lactamase / Beta-lactamase/transpeptidase-like / SN-GLYCEROL-3-PHOSPHATE / L(+)-TARTARIC ACID / Serine-type D-Ala-D-Ala carboxypeptidase
Function and homology information
Biological speciesLactiplantibacillus plantarum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 Å
AuthorsRavaud, S. / Nikolopoulos, N. / Grangeasse, C.
Funding support France, 2items
OrganizationGrant numberCountry
Centre National de la Recherche Scientifique (CNRS) France
Agence Nationale de la Recherche (ANR)18-CE15-0011 France
CitationJournal: Elife / Year: 2023
Title: Structure-function analysis of Lactiplantibacillus plantarum DltE& reveals D-alanylated lipoteichoic acids as direct cues supporting Drosophila juvenile growth.
Authors: Nikolopoulos, N. / Matos, R. / Ravaud, S. / Courtin, P. / Akherraz, H. / Palussiere, S. / Gueguen-Chaignon, V. / Salomon-Mallet, M. / Guillot, A. / Guerardel, Y. / Chapot-Chartier, M.P. / ...Authors: Nikolopoulos, N. / Matos, R. / Ravaud, S. / Courtin, P. / Akherraz, H. / Palussiere, S. / Gueguen-Chaignon, V. / Salomon-Mallet, M. / Guillot, A. / Guerardel, Y. / Chapot-Chartier, M.P. / Grangeasse, C. / Leulier, F.
History
DepositionJul 29, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 26, 2023Provider: repository / Type: Initial release
Revision 1.1Feb 7, 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: Beta-lactamase family protein
B: Beta-lactamase family protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)84,91011
Polymers83,6452
Non-polymers1,2659
Water9,620534
1
A: Beta-lactamase family protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,4095
Polymers41,8231
Non-polymers5864
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Beta-lactamase family protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,5016
Polymers41,8231
Non-polymers6785
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)48.678, 96.066, 150.828
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

#1: Protein Beta-lactamase family protein / Class A beta-lactamase-related serine hydrolase / Penicillin-binding protein PbpX / Serine-type D- ...Class A beta-lactamase-related serine hydrolase / Penicillin-binding protein PbpX / Serine-type D-Ala-D-Ala carboxypeptidase


Mass: 41822.508 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lactiplantibacillus plantarum (bacteria)
Gene: pbpX2, pbpX_4, C7M36_02596, E3O64_07015, E3U93_06380, FEE41_04205, IV39_GL001648, LPJSA22_01868, SN35N_2987
Production host: Escherichia coli (E. coli)
References: UniProt: A0A0P7JVD2, serine-type D-Ala-D-Ala carboxypeptidase
#2: Chemical ChemComp-TLA / L(+)-TARTARIC ACID / Tartaric acid


Mass: 150.087 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H6O6
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical
ChemComp-G3P / SN-GLYCEROL-3-PHOSPHATE / Glycerol 3-phosphate


Mass: 172.074 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H9O6P / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 534 / 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: 2.11 Å3/Da / Density % sol: 41.65 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: PEG 3350, ammonium tartrate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 2 / Wavelength: 0.98 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Nov 29, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.4→48.03 Å / Num. obs: 139817 / % possible obs: 99.98 % / Redundancy: 2 % / Biso Wilson estimate: 15.31 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.022 / Net I/σ(I): 16.61
Reflection shellResolution: 1.4→1.45 Å / Rmerge(I) obs: 0.4422 / Num. unique obs: 13770 / CC1/2: 0.678

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
PHENIX1.20.1_4487refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 8AGR

8agr


Resolution: 1.4→48.03 Å / SU ML: 0.1488 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 20.239
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1931 1053 -
Rwork0.1746 138759 -
obs0.1748 139812 99.98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 19.83 Å2
Refinement stepCycle: LAST / Resolution: 1.4→48.03 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4996 0 77 534 5607
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00895248
X-RAY DIFFRACTIONf_angle_d1.10637095
X-RAY DIFFRACTIONf_chiral_restr0.0769784
X-RAY DIFFRACTIONf_plane_restr0.0088907
X-RAY DIFFRACTIONf_dihedral_angle_d13.5939746
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.4-1.460.32271290.263117117X-RAY DIFFRACTION99.97
1.46-1.540.2531300.247317159X-RAY DIFFRACTION99.98
1.54-1.640.25421310.204817205X-RAY DIFFRACTION99.99
1.64-1.760.18581310.183117228X-RAY DIFFRACTION99.97
1.76-1.940.22611310.183717255X-RAY DIFFRACTION99.97
1.94-2.220.16731320.154117353X-RAY DIFFRACTION99.99
2.22-2.80.16521320.162317446X-RAY DIFFRACTION99.99
2.8-48.030.18631370.164617996X-RAY DIFFRACTION99.99

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