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- PDB-8bk3: Crystal structure of the transpeptidase LdtMt2 from Mycobacterium... -

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Basic information

Entry
Database: PDB / ID: 8bk3
TitleCrystal structure of the transpeptidase LdtMt2 from Mycobacterium tuberculosis in complex with diepoxide ketone 1
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-like / L,D-transpeptidase catalytic domain / Prokaryotic membrane lipoprotein lipid attachment site profile.
Similarity search - Domain/homology
NITRATE ION / 1-[(2~{S},3~{R})-3-phenyloxiran-2-yl]ethanone / L,D-transpeptidase 2
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.15 Å
Authorsde Munnik, M. / Schofield, C.J.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research Council (BBSRC) United Kingdom
CitationJournal: Chem.Commun.(Camb.) / Year: 2023
Title: alpha beta , alpha ' beta '-Diepoxyketones are mechanism-based inhibitors of nucleophilic cysteine enzymes.
Authors: de Munnik, M. / Lithgow, J. / Brewitz, L. / Christensen, K.E. / Bates, R.H. / Rodriguez-Miquel, B. / Schofield, C.J.
History
DepositionNov 8, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 22, 2023Provider: repository / Type: Initial release
Revision 1.1Oct 16, 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

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)76,73911
Polymers76,0182
Non-polymers7219
Water13,385743
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: mass spectrometry
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2490 Å2
ΔGint13 kcal/mol
Surface area31150 Å2
Unit cell
Length a, b, c (Å)60.933, 95.057, 75.535
Angle α, β, γ (deg.)90.00, 92.60, 90.00
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, 752 molecules

#2: Chemical ChemComp-QXU / 1-[(2~{S},3~{R})-3-phenyloxiran-2-yl]ethanone


Mass: 162.185 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H10O2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-NO3 / NITRATE ION


Mass: 62.005 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: NO3
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#6: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 743 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.87 Å3/Da / Density % sol: 57.21 %
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: May 6, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 2.15→75.47 Å / Num. obs: 46881 / % possible obs: 100 % / Redundancy: 7 % / CC1/2: 0.966 / Rmerge(I) obs: 0.167 / Rpim(I) all: 0.068 / Rrim(I) all: 0.181 / Net I/σ(I): 10.2
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
2.15-2.1971.3511.123070.7090.5591.4999.9
5.84-75.527.30.0593824210.9250.0260.064100

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation6.19 Å75.46 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: 2.15→75.46 Å / SU ML: 0.29 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 29.01 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2526 2279 4.92 %
Rwork0.216 --
obs0.2178 46328 98.83 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.15→75.46 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5250 0 46 743 6039
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0055524
X-RAY DIFFRACTIONf_angle_d0.5947575
X-RAY DIFFRACTIONf_dihedral_angle_d14.3121907
X-RAY DIFFRACTIONf_chiral_restr0.05842
X-RAY DIFFRACTIONf_plane_restr0.0041006
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.15-2.20.32371240.29932751X-RAY DIFFRACTION99
2.2-2.250.50241490.46052500X-RAY DIFFRACTION91
2.25-2.30.48921410.40992610X-RAY DIFFRACTION94
2.3-2.370.3491360.29072772X-RAY DIFFRACTION100
2.37-2.440.30331470.27592776X-RAY DIFFRACTION100
2.44-2.510.30451380.26972752X-RAY DIFFRACTION99
2.51-2.60.36151240.26982761X-RAY DIFFRACTION100
2.6-2.710.28481430.24742773X-RAY DIFFRACTION100
2.71-2.830.29271390.23432783X-RAY DIFFRACTION100
2.83-2.980.27031330.22142788X-RAY DIFFRACTION100
2.98-3.170.25111360.21332803X-RAY DIFFRACTION100
3.17-3.410.21741480.18452787X-RAY DIFFRACTION100
3.41-3.750.21610.18762755X-RAY DIFFRACTION100
3.76-4.30.18961560.1552792X-RAY DIFFRACTION100
4.3-5.410.19421540.14422796X-RAY DIFFRACTION100
5.42-75.460.2111500.19132850X-RAY DIFFRACTION100
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)
10.60430.0209-0.76060.8571.24674.65260.07280.1795-0.0448-0.18440.1074-0.0339-0.13260.1376-0.17390.22040.051-0.02140.25860.00680.222210.514-103.157717.2449
22.67610.02181.13011.3498-0.06012.25060.0671-0.28040.04670.1245-0.1028-0.0961-0.07960.03920.0360.2318-0.00890.04650.2310.00220.156913.309-92.139854.5374
30.60760.22290.72513.2445-1.79383.9767-0.0402-0.04910.1141-0.20970.04630.05350.0221-0.2141-0.00370.17250.00970.03250.1743-0.02740.2108-11.7435-80.3157-32.2604
40.51240.39720.36270.26050.1364.23450.08560.0924-0.03910.07270.0766-0.08380.08520.2696-0.15120.26150.1147-0.02040.3324-0.02530.234-10.7207-91.9173.8027
54.2141-0.7375-1.24010.48770.05680.52470.11280.5519-0.1269-0.1471-0.13210.11860.1441-0.77820.02010.370.002-0.07170.5923-0.02190.2156-24.3728-94.879813.4155
63.9070.2193-0.29280.1713-0.58092.47170.12140.2075-0.4685-0.1918-0.05940.15750.3325-0.4357-0.04760.36840.0081-0.05290.3204-0.06270.3169-27.4459-98.888418.1495
72.74141.72530.00085.38712.0320.96450.1461-0.2731-0.06480.4167-0.28290.09070.1468-0.37780.13470.34040.0005-0.01910.404-0.01880.183-20.9725-93.56226.2466
80.89860.4607-0.52810.92680.95465.69030.20820.3337-0.2483-0.0308-0.0703-0.08080.57270.4618-0.10640.42540.174-0.08320.4372-0.08580.2638-8.4939-99.51748.7602
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 57 through 248 )
2X-RAY DIFFRACTION2chain 'A' and (resid 249 through 407 )
3X-RAY DIFFRACTION3chain 'B' and (resid 57 through 157 )
4X-RAY DIFFRACTION4chain 'B' and (resid 158 through 289 )
5X-RAY DIFFRACTION5chain 'B' and (resid 290 through 308 )
6X-RAY DIFFRACTION6chain 'B' and (resid 309 through 341 )
7X-RAY DIFFRACTION7chain 'B' and (resid 342 through 368 )
8X-RAY DIFFRACTION8chain 'B' and (resid 369 through 407 )

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