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- PDB-8a1m: Crystal structure of the transpeptidase LdtMt2 from Mycobacterium... -

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Basic information

Entry
Database: PDB / ID: 8a1m
TitleCrystal structure of the transpeptidase LdtMt2 from Mycobacterium tuberculosis in complex with maleimide analogue 4
ComponentsL,D-transpeptidase 2
KeywordsANTIMICROBIAL PROTEIN / L / D-transpeptidase / LdtMt2 / Inhibitor / Covalent
Function / homology
Function and homology information


peptidoglycan-based cell wall biogenesis / peptidoglycan-protein cross-linking / peptidoglycan metabolic process / peptidoglycan L,D-transpeptidase activity / Transferases; Acyltransferases; Aminoacyltransferases / acyltransferase activity / peptidoglycan-based cell wall / cell wall organization / regulation of cell shape / extracellular region ...peptidoglycan-based cell wall biogenesis / peptidoglycan-protein cross-linking / peptidoglycan metabolic process / peptidoglycan L,D-transpeptidase activity / Transferases; Acyltransferases; Aminoacyltransferases / acyltransferase activity / peptidoglycan-based cell wall / cell wall organization / regulation of cell shape / extracellular region / 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
Chem-KUL / L,D-transpeptidase 2
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.3 Å
Authorsde Munnik, M. / Lang, P.A. / Brem, J. / Schofield, C.J.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research Council (BBSRC) United Kingdom
CitationJournal: Chem Sci / Year: 2023
Title: High-throughput screen with the l,d-transpeptidase Ldt Mt2 of Mycobacterium tuberculosis reveals novel classes of covalently reacting inhibitors.
Authors: de Munnik, M. / Lang, P.A. / De Dios Anton, F. / Cacho, M. / Bates, R.H. / Brem, J. / Rodriguez Miquel, B. / Schofield, C.J.
History
DepositionJun 1, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 14, 2023Provider: repository / Type: Initial release
Revision 1.1Aug 2, 2023Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Feb 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

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)77,44120
Polymers76,0182
Non-polymers1,42218
Water6,864381
1
A: L,D-transpeptidase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,91914
Polymers38,0091
Non-polymers91013
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: L,D-transpeptidase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,5226
Polymers38,0091
Non-polymers5135
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)61.700, 95.070, 75.450
Angle α, β, γ (deg.)90.000, 92.220, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 2 molecules AB

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


Mass: 38009.145 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Gene: ldtB, MT2594, V735_02606 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: O53223, Transferases; Acyltransferases; Aminoacyltransferases

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Non-polymers , 7 types, 399 molecules

#2: Chemical ChemComp-KUL / 1-(2-fluoranyl-5-methylsulfonyl-phenyl)pyrrolidine-2,5-dione / 1-(2-Fluoro-5-methylsulfonylphenyl)pyrrole-2,5-dione (reacted form of)


Mass: 271.265 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C11H10FNO4S / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical
ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#6: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Na
#7: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Formula: Cl
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 381 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.91 Å3/Da / Density % sol: 57.71 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / Details: 0.2 M Ammonium nitrate, 20% PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9763 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Jul 31, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 2.3→48.66 Å / Num. obs: 38184 / % possible obs: 98.6 % / Redundancy: 6.9 % / CC1/2: 0.991 / Rmerge(I) obs: 0.133 / Net I/σ(I): 9.6
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2% possible all
2.3-2.3671.2191.528510.66599.1
10.29-48.666.20.04127.54520.99398

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation6.17 Å75.4 Å

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Processing

Software
NameVersionClassificationNB
PHENIX1.18.2_3874refinement
XDSdata reduction
xia2data scaling
PHASER2.8.3phasing
PDB_EXTRACT3.27data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6RRM

6rrm


Resolution: 2.3→48.66 Å / SU ML: 0.34 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 29.02 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2492 1948 5.11 %
Rwork0.218 36167 -
obs0.2195 38115 98.36 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 163.79 Å2 / Biso mean: 53.2513 Å2 / Biso min: 28.42 Å2
Refinement stepCycle: final / Resolution: 2.3→48.66 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5237 0 81 382 5700
Biso mean--65.98 50.9 -
Num. residues----704
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.3-2.360.32881410.30242605274699
2.36-2.420.3841240.29392566269099
2.42-2.490.32431340.28362586272099
2.49-2.570.28141450.27552597274299
2.57-2.670.33331350.28612593272899
2.67-2.770.35231590.2892563272299
2.77-2.90.31971510.25632612276399
2.9-3.050.26761390.236125962735100
3.05-3.240.26951290.22542621275099
3.24-3.490.25511510.23492529268098
3.49-3.840.27621220.23372477259993
3.84-4.40.21091280.18422494262295
4.4-5.540.17761500.150126422792100
5.54-48.660.1981400.197126862826100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.35431.0293-0.2386.73772.38358.78680.0043-0.0161-0.00710.0557-0.08340.37610.1625-0.3040.04110.3020.03230.04010.42960.03060.348411.3915-110.74130.26
21.77240.11950.17081.05350.00213.06710.0463-0.11460.0521-0.1334-0.0482-0.1136-0.3420.1941-0.0020.38620.020.02980.2434-0.00460.360412.1777-94.110444.4794
35.65753.15840.38547.8226-1.80856.34820.2176-0.18730.39130.1809-0.12910.0248-0.124-0.085-0.0650.26970.02360.02720.22070.0030.3426-10.76-77.8327-33.5959
40.2182-0.73470.32012.1895-1.32574.5171-0.1248-0.1918-0.01030.25270.38850.13950.19460.0423-0.23110.30520.10530.02210.5020.01680.3712-12.1922-89.2646-14.0748
51.05760.5977-0.36350.34310.41477.0985-0.0158-0.1414-0.03850.35010.1214-0.14180.1030.0202-0.0570.60330.2366-0.09910.4897-0.01770.4637-11.1841-91.43059.0922
63.92441.0241-0.00070.30270.0460.03050.25630.2547-0.37940.0637-0.12760.1156-0.0361-0.5109-0.14090.81580.1949-0.02460.7331-0.04060.4987-26.3534-97.816414.6973
75.10731.3532-0.20773.8192-0.42750.06280.1151-0.4859-0.21460.4222-0.07760.39350.0892-0.5293-0.01010.94130.1697-0.01470.74660.05460.427-22.305-94.715625.3026
82.11991.0587-1.16833.38361.79954.89810.23650.2359-0.21230.173-0.0564-0.42050.39920.0306-0.20740.68550.3612-0.09160.6522-0.02710.4794-8.6102-99.77918.3017
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 55 through 144 )A55 - 144
2X-RAY DIFFRACTION2chain 'A' and (resid 145 through 407 )A145 - 407
3X-RAY DIFFRACTION3chain 'B' and (resid 57 through 122 )B57 - 122
4X-RAY DIFFRACTION4chain 'B' and (resid 123 through 212 )B123 - 212
5X-RAY DIFFRACTION5chain 'B' and (resid 213 through 289 )B213 - 289
6X-RAY DIFFRACTION6chain 'B' and (resid 290 through 334 )B290 - 334
7X-RAY DIFFRACTION7chain 'B' and (resid 335 through 368 )B335 - 368
8X-RAY DIFFRACTION8chain 'B' and (resid 369 through 407 )B369 - 407

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