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- PDB-7a1e: LppS with covalent adduct derived from 1c -

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Basic information

Entry
Database: PDB / ID: 7a1e
TitleLppS with covalent adduct derived from 1c
ComponentsL,D-transpeptidase 2
KeywordsLIGASE / Transpeptidase / cell wall / peptidoglycan / antibiotic / Beta-lactam / Covalent inhibitor / Mycobacterium tuberculosis
Function / homology
Function and homology information


peptidoglycan-protein cross-linking / peptidoglycan L,D-transpeptidase activity / Transferases; Acyltransferases; Aminoacyltransferases / acyltransferase activity / cell wall organization / regulation of cell shape / metal ion binding / plasma membrane
Similarity search - Function
Bacterial Ig domain, transpeptidase-associated / Bacterial Ig domain / : / L,D-transpeptidase (L,D-TPase) catalytic domain profile. / L,D-transpeptidase catalytic domain / L,D-transpeptidase catalytic domain / L,D-transpeptidase catalytic domain-like / Prokaryotic membrane lipoprotein lipid attachment site profile.
Similarity search - Domain/homology
ACETATE ION / phenylmethanethiol / L,D-transpeptidase 2
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.77 Å
AuthorsSchnell, R. / Steiner, E.M.
Funding support Sweden, 1items
OrganizationGrant numberCountry
Vinnova Sweden
CitationJournal: Cell Chem Biol / Year: 2021
Title: N-Thio-beta-lactams targeting L,D-transpeptidase-2, with activity against drug-resistant strains of Mycobacterium tuberculosis.
Authors: Martelli, G. / Pessatti, T.B. / Steiner, E.M. / Cirillo, M. / Caso, C. / Bisognin, F. / Landreh, M. / Monte, P.D. / Giacomini, D. / Schnell, R.
History
DepositionAug 12, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 21, 2021Provider: repository / Type: Initial release
Revision 1.1Sep 29, 2021Group: Database references / Category: citation / database_2
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
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

Downloads & links

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Assembly

Deposited unit
A: L,D-transpeptidase 2
B: L,D-transpeptidase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,7997
Polymers56,4392
Non-polymers3605
Water9,818545
1
A: L,D-transpeptidase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,4624
Polymers28,2191
Non-polymers2423
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: L,D-transpeptidase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,3373
Polymers28,2191
Non-polymers1182
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)50.309, 74.873, 67.764
Angle α, β, γ (deg.)90.000, 111.520, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein L,D-transpeptidase 2 / LDT 2 / Ldt(Mt2)


Mass: 28219.289 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: The construct used here contains two domains: domain-B (Ig-like) and domain-C (catalytic transpeptidase domain), residue range 149-408 of the full length protein.
Source: (gene. exp.) Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv) (bacteria)
Strain: ATCC 25618 / H37Rv / Gene: ldtB, lppS, Rv2518c, RVBD_2518c, P425_02624 / Plasmid: pNIC28-Bsa4
Details (production host): N-terminal His6-tag, removable by TEV cleavage
Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: I6Y9J2, Transferases; Acyltransferases; Aminoacyltransferases
#2: Chemical ChemComp-SDQ / phenylmethanethiol


Mass: 124.203 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H8S / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H3O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 545 / 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: 2.1 Å3/Da / Density % sol: 41.53 % / Description: rod
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.25
Details: Well solution: 0.1 M Na-Citrate pH 4.25 / 17.5% PEG 6K The ligand was added to the soaking solution at 4 mM concentration. In the soaking drop, Citrate is replaced by Acetate (0.3 M) 150 mM ...Details: Well solution: 0.1 M Na-Citrate pH 4.25 / 17.5% PEG 6K The ligand was added to the soaking solution at 4 mM concentration. In the soaking drop, Citrate is replaced by Acetate (0.3 M) 150 mM NaCl 0.1 M Bis-Tris pH 6.2 0.3 M Na-Acetate pH 5.2 25% PEG 6K PEG 6K INCREASED to 25% FOR CRYO-PROTECTION

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: MAX IV / Beamline: BioMAX / Wavelength: 0.82656 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 28, 2019 / Details: mirrors (VFM, HFM)
RadiationMonochromator: Si(111) double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.82656 Å / Relative weight: 1
ReflectionResolution: 1.77→25.15 Å / Num. obs: 45504 / % possible obs: 99.7 % / Observed criterion σ(I): 2.1 / Redundancy: 6.9 % / Biso Wilson estimate: 17.8 Å2 / Rmerge(I) obs: 0.088 / Net I/σ(I): 10.1
Reflection shellResolution: 1.77→1.81 Å / Redundancy: 6.3 % / Rmerge(I) obs: 0.658 / Mean I/σ(I) obs: 2.1 / Num. unique obs: 2459 / % possible all: 94.5

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Processing

Software
NameVersionClassification
REFMAC5.8.0103refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5LBG

5lbg


Resolution: 1.77→25 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.946 / SU B: 3.106 / SU ML: 0.096 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.127 / ESU R Free: 0.126 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.214 2236 4.9 %RANDOM
Rwork0.165 ---
obs0.167 43132 99.4 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 93.17 Å2 / Biso mean: 29.57 Å2 / Biso min: 14.44 Å2
Baniso -1Baniso -2Baniso -3
1--2.2 Å20 Å20.85 Å2
2---0.26 Å20 Å2
3---1.37 Å2
Refinement stepCycle: final / Resolution: 1.77→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3982 0 24 545 4551
Biso mean--31.85 37.51 -
Num. residues----518
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0194129
X-RAY DIFFRACTIONr_bond_other_d0.0020.023739
X-RAY DIFFRACTIONr_angle_refined_deg1.6991.9175643
X-RAY DIFFRACTIONr_angle_other_deg1.0363.0018585
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.965520
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.06424.421190
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.63915594
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.5851520
X-RAY DIFFRACTIONr_chiral_restr0.1070.2607
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0214805
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02975
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.77→1.82 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.283 137 -
Rwork0.25 3038 -
all-3175 -
obs--95.09 %

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