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- PDB-8a1n: Crystal structure of the transpeptidase LdtMt2 from Mycobacterium... -

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Basic information

Entry
Database: PDB / ID: 8a1n
TitleCrystal structure of the transpeptidase LdtMt2 from Mycobacterium tuberculosis in complex with fumaryl amide analogue 13
ComponentsL,D-transpeptidase 2
KeywordsANTIMICROBIAL PROTEIN / L / D-transpeptidase / 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-KUS / L,D-transpeptidase 2
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.05 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)76,72511
Polymers76,0182
Non-polymers7069
Water10,791599
1
A: L,D-transpeptidase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,5137
Polymers38,0091
Non-polymers5046
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: L,D-transpeptidase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,2114
Polymers38,0091
Non-polymers2023
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)60.929, 94.633, 75.356
Angle α, β, γ (deg.)90.000, 92.350, 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 , 6 types, 608 molecules

#2: Chemical ChemComp-KUS / (Z)-N-(4-chlorophenyl)-4-oxidanylidene-but-2-enamide / N1-(4-chlorophenyl)-2-butenediamide (reacted form of)


Mass: 209.629 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H8ClNO2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#5: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: Na
#6: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 599 / 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: 2.86 Å3/Da / Density % sol: 56.92 %
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: Feb 26, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 2.05→75.3 Å / Num. obs: 53680 / % possible obs: 100 % / Redundancy: 6.8 % / CC1/2: 0.999 / Rmerge(I) obs: 0.09 / Rpim(I) all: 0.037 / Rrim(I) all: 0.097 / Net I/σ(I): 13.2
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
2.05-2.096.80.8211.126740.7730.3380.88999.9
5.56-75.357.10.03353.727410.9990.0130.03599.8

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation6.2 Å75.29 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: 2.05→75.29 Å / SU ML: 0.25 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 24.62 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2392 2547 4.75 %
Rwork0.1929 51056 -
obs0.1951 53603 99.75 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 126.74 Å2 / Biso mean: 44.3746 Å2 / Biso min: 18.95 Å2
Refinement stepCycle: final / Resolution: 2.05→75.29 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5227 0 42 599 5868
Biso mean--53.53 46.28 -
Num. residues----700
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 18

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.05-2.090.30571300.26962806293698
2.09-2.130.31291500.264527762926100
2.13-2.180.29671810.26427902971100
2.18-2.230.29191410.245128222963100
2.23-2.280.30091330.260228662999100
2.28-2.350.24821340.225228322966100
2.35-2.410.25231450.21728082953100
2.41-2.490.29311410.213828442985100
2.49-2.580.24061460.213528202966100
2.58-2.680.25141470.214628222969100
2.68-2.810.33011670.215828162983100
2.81-2.950.29691370.212328442981100
2.95-3.140.27041430.203128322975100
3.14-3.380.21971020.189728902992100
3.38-3.720.21541220.18328582980100
3.72-4.260.21931340.157528602994100
4.26-5.370.17361340.14128863020100
5.37-75.290.2111600.19372884304499
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)
12.66521.667-1.40953.2212.06774.74790.027-0.1566-0.1891-0.1703-0.15110.0290.0344-0.34080.19890.29810.065-0.02690.4743-0.00370.337210.3543-111.08841.2651
20.05550.0273-0.54533.0763.32248.84990.00410.16510.0162-0.39380.3452-0.0199-0.2660.0967-0.32590.24630.0429-0.00040.49130.0180.363115.0546-105.38556.3927
30.98640.13670.66720.95680.67293.63810.1241-0.0168-0.0506-0.05780.0007-0.04040.04940.0518-0.12290.23940.04950.00570.20910.01540.30667.9036-96.556139.6721
42.8207-0.42950.86411.3717-0.62842.77090.0899-0.26230.16420.0338-0.1188-0.1368-0.16060.25090.02990.2468-0.00480.01680.2358-0.01650.243515.727-91.024652.6381
52.31911.70820.68337.6082-2.22154.78680.1295-0.28310.16820.125-0.22220.044-0.1307-0.09960.0820.19150.01980.00150.231-0.04340.3059-10.7046-77.8063-33.3018
60.18940.5495-0.72173.1693-2.43275.5678-0.04440.02820.0697-0.31070.310.19250.128-0.2707-0.16430.18520.0135-0.03320.40540.0190.3295-14.4257-84.0668-31.0033
70.46630.3160.55690.15040.3584.3920.10040.19-0.04530.110.143-0.07190.22350.5542-0.23150.36820.1576-0.02550.4445-0.01670.3552-10.7275-91.92213.3365
82.3023-0.2670.22991.23110.46152.52740.31080.2539-0.31750.0452-0.21710.01750.492-0.0254-0.08980.4970.1323-0.09730.3811-0.03280.345-19.1147-97.27615.9926
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 58 through 110 )A58 - 110
2X-RAY DIFFRACTION2chain 'A' and (resid 111 through 157 )A111 - 157
3X-RAY DIFFRACTION3chain 'A' and (resid 158 through 289 )A158 - 289
4X-RAY DIFFRACTION4chain 'A' and (resid 290 through 407 )A290 - 407
5X-RAY DIFFRACTION5chain 'B' and (resid 58 through 122 )B58 - 122
6X-RAY DIFFRACTION6chain 'B' and (resid 123 through 157 )B123 - 157
7X-RAY DIFFRACTION7chain 'B' and (resid 158 through 289 )B158 - 289
8X-RAY DIFFRACTION8chain 'B' and (resid 290 through 407 )B290 - 407

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