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- PDB-8aji: Crystal structure of DltE from L. plantarum, TCEP form -

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Basic information

Entry
Database: PDB / ID: 8aji
TitleCrystal structure of DltE from L. plantarum, TCEP 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 / 3,3',3''-phosphanetriyltripropanoic acid / 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: 1.94 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 28, 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
C: Beta-lactamase family protein
D: Beta-lactamase family protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)169,22515
Polymers167,2904
Non-polymers1,93511
Water21,7981210
1
A: Beta-lactamase family protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,4655
Polymers41,8231
Non-polymers6424
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Beta-lactamase family protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,2233
Polymers41,8231
Non-polymers4002
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Beta-lactamase family protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,2233
Polymers41,8231
Non-polymers4002
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Beta-lactamase family protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,3154
Polymers41,8231
Non-polymers4923
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)76.236, 98.642, 135.934
Angle α, β, γ (deg.)90.000, 105.799, 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.: 4
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-TCE / 3,3',3''-phosphanetriyltripropanoic acid / 3-[bis(2-carboxyethyl)phosphanyl]propanoic acid / TCEP


Mass: 250.186 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C9H15O6P / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-TLA / L(+)-TARTARIC ACID / Tartaric acid


Mass: 150.087 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C4H6O6
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1210 / 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: 2.94 Å3/Da / Density % sol: 58.16 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: PEG 3350, ammonium tartrate, TCEP HCl

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.87313 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Apr 18, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.87313 Å / Relative weight: 1
ReflectionResolution: 1.94→49.501 Å / Num. obs: 139757 / % possible obs: 97.7 % / Redundancy: 3.8 % / CC1/2: 0.988 / Rmerge(I) obs: 0.095 / Net I/σ(I): 5.3
Reflection shellResolution: 1.94→1.97 Å / Rmerge(I) obs: 0.395 / Num. unique obs: 6771 / CC1/2: 0.811

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Processing

Software
NameVersionClassification
REFMAC5.8.0352refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 8AGR

8agr


Resolution: 1.94→49.501 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.932 / SU B: 3.33 / SU ML: 0.095 / Cross valid method: FREE R-VALUE / ESU R: 0.131 / ESU R Free: 0.123
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2124 1994 1.427 %
Rwork0.1833 137699 -
all0.184 --
obs-139693 97.569 %
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: 24.243 Å2
Baniso -1Baniso -2Baniso -3
1--0.014 Å20 Å2-0.003 Å2
2--0.001 Å2-0 Å2
3---0.013 Å2
Refinement stepCycle: LAST / Resolution: 1.94→49.501 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10510 0 126 1210 11846
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.01110949
X-RAY DIFFRACTIONr_bond_other_d0.0360.0169975
X-RAY DIFFRACTIONr_angle_refined_deg1.3971.64414784
X-RAY DIFFRACTIONr_angle_other_deg0.7741.55523297
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.03151379
X-RAY DIFFRACTIONr_dihedral_angle_2_deg6.6351043
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.611101929
X-RAY DIFFRACTIONr_dihedral_angle_6_deg17.70610487
X-RAY DIFFRACTIONr_chiral_restr0.0760.21655
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0212381
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022139
X-RAY DIFFRACTIONr_nbd_refined0.230.22043
X-RAY DIFFRACTIONr_symmetry_nbd_other0.20.28389
X-RAY DIFFRACTIONr_nbtor_refined0.1830.25422
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0780.25716
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1550.2893
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.1540.22
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.180.219
X-RAY DIFFRACTIONr_nbd_other0.2470.257
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.2160.221
X-RAY DIFFRACTIONr_mcbond_it2.2862.5025423
X-RAY DIFFRACTIONr_mcbond_other2.2842.5025423
X-RAY DIFFRACTIONr_mcangle_it3.0863.7356782
X-RAY DIFFRACTIONr_mcangle_other3.0863.7366783
X-RAY DIFFRACTIONr_scbond_it3.2672.9085526
X-RAY DIFFRACTIONr_scbond_other3.2672.9095527
X-RAY DIFFRACTIONr_scangle_it4.9034.2067985
X-RAY DIFFRACTIONr_scangle_other4.9024.2067986
X-RAY DIFFRACTIONr_lrange_it6.55434.88212572
X-RAY DIFFRACTIONr_lrange_other6.47333.03512261
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.94-1.990.2511400.2459870X-RAY DIFFRACTION95.2154
1.99-2.0450.2621400.239719X-RAY DIFFRACTION95.8115
2.045-2.1040.2571380.2189508X-RAY DIFFRACTION96.3059
2.104-2.1690.2571310.2139237X-RAY DIFFRACTION96.7369
2.169-2.240.2441260.2059040X-RAY DIFFRACTION97.1077
2.24-2.3180.2051300.1918639X-RAY DIFFRACTION96.8308
2.318-2.4050.2571230.1878464X-RAY DIFFRACTION97.5463
2.405-2.5030.2481130.1848109X-RAY DIFFRACTION97.3709
2.503-2.6140.231130.1787793X-RAY DIFFRACTION97.4605
2.614-2.7410.2221100.1787503X-RAY DIFFRACTION97.8535
2.741-2.8890.2241050.1717190X-RAY DIFFRACTION98.5278
2.889-3.0640.222990.1716803X-RAY DIFFRACTION98.7835
3.064-3.2750.222930.1786419X-RAY DIFFRACTION99.072
3.275-3.5360.208880.1795978X-RAY DIFFRACTION99.0206
3.536-3.8710.166820.1655551X-RAY DIFFRACTION99.1202
3.871-4.3250.165730.1524997X-RAY DIFFRACTION99.1396
4.325-4.9870.147640.1534442X-RAY DIFFRACTION99.273
4.987-6.0930.217580.1983759X-RAY DIFFRACTION99.6346
6.093-8.5520.215430.1992976X-RAY DIFFRACTION99.7357

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