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- PDB-8a1l: Crystal structure of the transpeptidase LdtMt2 from Mycobacterium... -

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Basic information

Entry
Database: PDB / ID: 8a1l
TitleCrystal structure of the transpeptidase LdtMt2 from Mycobacterium tuberculosis in complex with alpha-chloro ketone 2
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
Immunoglobulin-like - #3780 / 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 ...Immunoglobulin-like - #3780 / 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
Chem-KS9 / 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
Revision 1.3Oct 23, 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)77,25316
Polymers76,0182
Non-polymers1,23414
Water7,620423
1
A: L,D-transpeptidase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,6418
Polymers38,0091
Non-polymers6327
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: L,D-transpeptidase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,6118
Polymers38,0091
Non-polymers6027
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)61.756, 94.772, 75.745
Angle α, β, γ (deg.)90.000, 92.900, 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, 437 molecules

#2: Chemical ChemComp-KS9 / (phenylmethyl) N-[(3S,4S)-4-methyl-2-oxidanylidene-hexan-3-yl]carbamate / benzyl ((3S,4R)-1-chloro-4-methyl-2-oxohexan-3-yl)carb (reacted form of)


Mass: 263.332 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C15H21NO3 / 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.: 4 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#5: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#6: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#7: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: Cl
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 423 / 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: 2.91 Å3/Da / Density % sol: 57.76 %
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→61.5 Å / Num. obs: 38421 / % possible obs: 99.8 % / Redundancy: 6.9 % / CC1/2: 0.97 / Rmerge(I) obs: 0.163 / Rpim(I) all: 0.068 / Rrim(I) all: 0.177 / Net I/σ(I): 9.8
Reflection shell

Diffraction-ID: 1 / % possible all: 100

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all
2.3-2.347.21.360.918940.7980.5491.468
6.24-61.536.90.05536.419780.9250.0250.061

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation6.18 Å75.58 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→51.69 Å / SU ML: 0.37 / Cross valid method: THROUGHOUT / σ(F): 1.39 / Phase error: 28.97 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2472 1951 5.1 %
Rwork0.2143 36322 -
obs0.216 38273 99.21 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 141.23 Å2 / Biso mean: 47.1036 Å2 / Biso min: 27.33 Å2
Refinement stepCycle: final / Resolution: 2.3→51.69 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5230 0 76 423 5729
Biso mean--55.35 46.45 -
Num. residues----705
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 (%)
2.3-2.360.35751370.3182514265197
2.36-2.430.35331230.28452581270499
2.43-2.50.30051290.27125962725100
2.5-2.580.30521510.2662604275599
2.58-2.670.30841280.270225932721100
2.67-2.780.36321760.267625522728100
2.78-2.90.31071410.259426032744100
2.9-3.060.28831480.238525932741100
3.06-3.250.22811200.223126342754100
3.25-3.50.2531500.20925942744100
3.5-3.850.25431280.23342535266396
3.85-4.410.21131320.170626202752100
4.41-5.550.15491510.150526272778100
5.55-51.690.21271370.195426762813100
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)
10.4503-0.1004-0.26160.40411.09683.91810.10570.1440.057-0.1089-0.0337-0.0419-0.2187-0.0471-0.06340.33810.056-0.00510.35740.06860.36749.9329-101.325124.4036
23.2486-1.5622-0.41683.06670.3342.7976-0.0019-0.15680.78660.0858-0.0725-0.605-0.5191.07980.03390.382-0.1337-0.00660.53070.0820.469422.5009-90.001252.6865
32.8428-0.73741.55062.8023-1.50694.9120.1345-0.27270.2593-0.041-0.2437-0.2263-0.18320.31440.10490.2102-0.02030.03350.30540.01460.328310.9628-91.278553.1465
41.79261.09221.91226.9408-1.16116.0330.16560.15210.191-0.4802-0.07680.1611-0.0818-0.2604-0.10260.26340.06330.0540.29450.02370.3285-10.3805-78.0243-35.7313
50.4095-0.05770.12171.6952-0.10091.9641-0.108-0.1595-0.06550.30330.2852-0.1457-0.06040.1279-0.17320.26730.105-0.02550.5103-0.03540.3573-12.1442-92.03291.8236
63.37210.55510.45010.9456-0.6390.647-0.0967-0.0047-0.07580.35780.25950.04070.0577-0.2517-0.16930.49890.14050.02260.6743-0.01480.3825-27.6683-98.605615.5265
70.95320.68380.90161.5603-0.62363.3021-0.0217-0.3077-0.23580.52540.1572-0.0317-0.0444-0.3303-0.15040.53190.2806-0.03540.6952-0.00570.4095-16.0181-97.428116.9274
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 57 through 289 )A57 - 289
2X-RAY DIFFRACTION2chain 'A' and (resid 290 through 334 )A290 - 334
3X-RAY DIFFRACTION3chain 'A' and (resid 335 through 407 )A335 - 407
4X-RAY DIFFRACTION4chain 'B' and (resid 57 through 144 )B57 - 144
5X-RAY DIFFRACTION5chain 'B' and (resid 145 through 289 )B145 - 289
6X-RAY DIFFRACTION6chain 'B' and (resid 290 through 334 )B290 - 334
7X-RAY DIFFRACTION7chain 'B' and (resid 335 through 407 )B335 - 407

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