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- PDB-7a11: LppS with covalent adduct derived from 1E -

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Basic information

Entry
Database: PDB / ID: 7a11
TitleLppS with covalent adduct derived from 1E
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
Immunoglobulin-like - #3710 / Bacterial Ig domain, transpeptidase-associated / Bacterial Ig domain / L,D-transpeptidase catalytic domain-like / L,D-transpeptidase catalytic domain-like / : / L,D-transpeptidase (L,D-TPase) catalytic domain profile. / L,D-transpeptidase catalytic domain / L,D-transpeptidase catalytic domain-like / L,D-transpeptidase catalytic domain ...Immunoglobulin-like - #3710 / Bacterial Ig domain, transpeptidase-associated / Bacterial Ig domain / L,D-transpeptidase catalytic domain-like / L,D-transpeptidase catalytic domain-like / : / L,D-transpeptidase (L,D-TPase) catalytic domain profile. / L,D-transpeptidase catalytic domain / L,D-transpeptidase catalytic domain-like / L,D-transpeptidase catalytic domain / Prokaryotic membrane lipoprotein lipid attachment site profile. / Beta Barrel / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
ACETATE ION / propane-1-thiol / L,D-transpeptidase 2
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.65 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 11, 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
Revision 1.3Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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)56,8108
Polymers56,4392
Non-polymers3716
Water9,674537
1
A: L,D-transpeptidase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,4144
Polymers28,2191
Non-polymers1943
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: L,D-transpeptidase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,3964
Polymers28,2191
Non-polymers1773
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)50.563, 74.552, 67.253
Angle α, β, γ (deg.)90.000, 111.780, 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-XL3 / propane-1-thiol


Mass: 76.161 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8S / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H3O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 537 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

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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: 2.09 Å3/Da / Density % sol: 41.02 % / 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 JM12 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. ...Details: Well solution: 0.1 M Na-Citrate pH 4.25 / 17.5% PEG 6K JM12 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: Mar 27, 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: 1.65→39.73 Å / Num. obs: 55802 / % possible obs: 100 % / Observed criterion σ(I): 1.8 / Redundancy: 7 % / Biso Wilson estimate: 21.6 Å2 / Rmerge(I) obs: 0.059 / Net I/σ(I): 14.2
Reflection shellResolution: 1.65→1.68 Å / Rmerge(I) obs: 0.931 / Mean I/σ(I) obs: 1.8 / Num. unique obs: 2746 / % possible all: 100

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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: 1.65→38 Å / Cor.coef. Fo:Fc: 0.973 / Cor.coef. Fo:Fc free: 0.955 / SU B: 2.261 / SU ML: 0.075 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.1 / ESU R Free: 0.102 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.207 2745 4.9 %RANDOM
Rwork0.164 ---
obs0.166 53027 99.9 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 84.86 Å2 / Biso mean: 27.62 Å2 / Biso min: 12.09 Å2
Baniso -1Baniso -2Baniso -3
1--1.13 Å20 Å20.12 Å2
2--0.29 Å20 Å2
3---0.56 Å2
Refinement stepCycle: final / Resolution: 1.65→38 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3982 0 24 537 4543
Biso mean--31.69 37.19 -
Num. residues----518
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0194155
X-RAY DIFFRACTIONr_bond_other_d0.0030.023767
X-RAY DIFFRACTIONr_angle_refined_deg1.811.9155683
X-RAY DIFFRACTIONr_angle_other_deg1.0663.0018655
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0175528
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.33324.456193
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.37915601
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.2831520
X-RAY DIFFRACTIONr_chiral_restr0.1140.2611
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.0214846
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02980
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: 1.65→1.69 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.292 203 -
Rwork0.262 3910 -
all-4113 -
obs--99.88 %

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