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- PDB-8agr: Crystal structure of DltE from L. plantarum, apo form -

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Basic information

Entry
Database: PDB / ID: 8agr
TitleCrystal structure of DltE from L. plantarum, apo form
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 / Serine-type D-Ala-D-Ala carboxypeptidase
Function and homology information
Biological speciesLactiplantibacillus plantarum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.86 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 20, 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)84,1819
Polymers83,6452
Non-polymers5367
Water15,223845
1
A: Beta-lactamase family protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,2016
Polymers41,8231
Non-polymers3785
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Beta-lactamase family protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,9813
Polymers41,8231
Non-polymers1582
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)60.874, 95.719, 68.013
Angle α, β, γ (deg.)90.000, 96.260, 90.000
Int Tables number4
Space group name H-MP1211

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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-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 845 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.35 Å3/Da / Density % sol: 47.77 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: PEG MME 5K, Tris pH8.5, LiSO4, ethylene glycol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.8731 Å
DetectorType: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Apr 18, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8731 Å / Relative weight: 1
ReflectionResolution: 1.86→47.86 Å / Num. obs: 64951 / % possible obs: 99.9 % / Redundancy: 4.5 % / Rpim(I) all: 0.12 / Net I/σ(I): 6.4
Reflection shellResolution: 1.86→1.9 Å / Mean I/σ(I) obs: 2 / Num. unique obs: 39993 / Rpim(I) all: 0.441

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Processing

Software
NameVersionClassification
REFMAC5.8.0352refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3WWX

3wwx


Resolution: 1.86→47.796 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.941 / WRfactor Rfree: 0.202 / WRfactor Rwork: 0.165 / SU B: 2.901 / SU ML: 0.086 / Average fsc free: 0.9732 / Average fsc work: 0.9822 / Cross valid method: FREE R-VALUE / ESU R: 0.126 / ESU R Free: 0.12
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2027 3142 4.84 %
Rwork0.1663 61780 -
all0.168 --
obs-64922 99.826 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 14.051 Å2
Baniso -1Baniso -2Baniso -3
1--0.013 Å20 Å20.008 Å2
2--0.006 Å20 Å2
3---0.005 Å2
Refinement stepCycle: LAST / Resolution: 1.86→47.796 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5058 0 31 845 5934
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0115268
X-RAY DIFFRACTIONr_bond_other_d0.0310.0164779
X-RAY DIFFRACTIONr_angle_refined_deg1.3531.6437127
X-RAY DIFFRACTIONr_angle_other_deg0.7121.55411167
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1725673
X-RAY DIFFRACTIONr_dihedral_angle_2_deg8.7981020
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.68410931
X-RAY DIFFRACTIONr_dihedral_angle_6_deg17.06110242
X-RAY DIFFRACTIONr_chiral_restr0.0670.2793
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.025981
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021039
X-RAY DIFFRACTIONr_nbd_refined0.2250.2903
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1920.23851
X-RAY DIFFRACTIONr_nbtor_refined0.180.22556
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0760.22657
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1610.2584
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0670.28
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2410.213
X-RAY DIFFRACTIONr_nbd_other0.2670.252
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1650.231
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.0160.21
X-RAY DIFFRACTIONr_mcbond_it1.2911.3812616
X-RAY DIFFRACTIONr_mcbond_other1.2871.3812616
X-RAY DIFFRACTIONr_mcangle_it1.8882.063274
X-RAY DIFFRACTIONr_mcangle_other1.8892.0613275
X-RAY DIFFRACTIONr_scbond_it2.4771.6992652
X-RAY DIFFRACTIONr_scbond_other2.4771.6992653
X-RAY DIFFRACTIONr_scangle_it3.8062.4263838
X-RAY DIFFRACTIONr_scangle_other3.8062.4263839
X-RAY DIFFRACTIONr_lrange_it5.52924.246138
X-RAY DIFFRACTIONr_lrange_other5.52824.2416139
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
1.86-1.9080.3162160.26245440.26447650.9570.96799.89510.263
1.908-1.960.2642230.22844810.22947110.9610.97299.85140.226
1.96-2.0170.2552190.19242730.19544950.9630.97899.93330.187
2.017-2.0790.212360.17541740.17744130.9740.98299.9320.17
2.079-2.1470.2132080.16740750.16942900.9740.98399.83680.162
2.147-2.2220.2212180.1639030.16341250.9710.98599.9030.155
2.222-2.3060.191780.15738040.15939860.9770.98699.89970.153
2.306-2.40.2161790.15536590.15838420.9710.98699.89590.15
2.4-2.5060.1991710.15335170.15536920.9750.98699.89170.149
2.506-2.6280.21460.15233700.15435180.9750.98699.94310.147
2.628-2.770.2121800.15132050.15433880.9730.98699.91150.147
2.77-2.9380.1971550.15929930.16131550.9760.98599.77810.156
2.938-3.140.1921770.16228080.16329890.9790.98599.86620.16
3.14-3.390.1791420.15626570.15828010.9820.98799.92860.155
3.39-3.7120.1911150.1524360.15225560.9820.98899.80440.151
3.712-4.1470.1441030.13222210.13323300.9890.9999.74250.135
4.147-4.7820.144970.13819670.13820750.9890.9999.46990.145
4.782-5.8420.277710.19116570.19417360.9750.98599.53920.199
5.842-8.2010.251720.22312890.22413680.9720.97799.48830.232
8.201-47.7960.132360.2147470.2097950.9910.96698.49060.227

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