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- PDB-8a1k: Crystal structure of the transpeptidase LdtMt2 from Mycobacterium... -

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Basic information

Entry
Database: PDB / ID: 8a1k
TitleCrystal structure of the transpeptidase LdtMt2 from Mycobacterium tuberculosis in complex with ebsulfur analogue 15
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-KT6 / L,D-transpeptidase 2
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.75 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 1.3Nov 13, 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)76,7768
Polymers76,0182
Non-polymers7586
Water17,853991
1
A: L,D-transpeptidase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,3373
Polymers38,0091
Non-polymers3282
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: L,D-transpeptidase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,4385
Polymers38,0091
Non-polymers4294
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)60.977, 95.169, 75.624
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 , 5 types, 997 molecules

#2: Chemical ChemComp-KT6 / 4,5-bis(chloranyl)-N-(2-hydroxyethyl)-2-sulfanyl-benzamide / 5,6-Dichloro-2-(2-hydroxyethyl)-1,2-benzisothiazol-3-one (reacted form of)


Mass: 266.144 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C9H9Cl2NO2S / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#5: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: Na
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 991 / 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: 2.88 Å3/Da / Density % sol: 57.35 %
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 23, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 1.75→60.9 Å / Num. obs: 86825 / % possible obs: 100 % / Redundancy: 6.6 % / CC1/2: 0.997 / Rmerge(I) obs: 0.063 / Rpim(I) all: 0.027 / Rrim(I) all: 0.069 / Net I/σ(I): 17.7
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
1.75-1.786.60.773143230.7940.3260.84100
4.75-60.947.10.02877.744300.9910.0120.0399.7

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation6.18 Å60.98 Å

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Processing

Software
NameVersionClassificationNB
PHENIX1.15.2_3472refinement
XDSdata reduction
xia2data scaling
PHASER2.8.3phasing
PDB_EXTRACT3.27data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6RRM

6rrm


Resolution: 1.75→48.409 Å / SU ML: 0.22 / Cross valid method: THROUGHOUT / σ(F): 1.37 / Phase error: 22.53 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2042 4357 5.03 %
Rwork0.1747 82241 -
obs0.1763 86598 99.72 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 99.6 Å2 / Biso mean: 34.6294 Å2 / Biso min: 14.19 Å2
Refinement stepCycle: final / Resolution: 1.75→48.409 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5212 0 43 991 6246
Biso mean--40.01 43.27 -
Num. residues----700
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.7502-1.77010.31521360.2911271798
1.7701-1.79090.25841310.2555275799
1.7909-1.81270.30871280.25012685100
1.8127-1.83570.27361620.24312754100
1.8357-1.85980.26431400.23482712100
1.8598-1.88530.23951430.22832735100
1.8853-1.91220.33231470.2695273699
1.9122-1.94080.39421360.3587272799
1.9408-1.97110.29831360.22332717100
1.9711-2.00340.22931410.20562728100
2.0034-2.0380.21541430.19762734100
2.038-2.0750.22781380.1948273999
2.075-2.11490.22081530.18132751100
2.1149-2.15810.23881490.18372709100
2.1581-2.2050.23081360.19732768100
2.205-2.25630.31141470.26292738100
2.2563-2.31280.2641340.20842716100
2.3128-2.37530.20711580.1792741100
2.3753-2.44520.23171440.17332770100
2.4452-2.52410.19951520.16732720100
2.5241-2.61430.21421220.16322764100
2.6143-2.7190.21011420.17212751100
2.719-2.84270.23371450.16812723100
2.8427-2.99260.2081430.16172788100
2.9926-3.180.19431610.16452738100
3.18-3.42550.20511480.1542767100
3.4255-3.77010.17541550.15022746100
3.7701-4.31530.15461460.13162768100
4.3153-5.43570.13991650.12412756100
5.4357-48.4090.17531760.184278699
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)
16.29191.26970.29745.05010.90754.48580.0613-0.1486-0.2102-0.46650.10980.4441-0.1765-0.6966-0.17820.32080.015-0.02820.39960.05370.32228.0826-9.72520.9506
21.02772.4818-1.20699.17261.70958.1422-0.1605-0.2557-0.17370.01140.2050.04190.0929-0.0628-0.03360.20420.06370.00510.3548-0.00020.246711.9065-19.62761.1535
30.87050.2819-0.08881.85362.13867.62390.05810.2324-0.1073-0.30410.5037-0.0228-0.20560.3453-0.47490.21690.0253-0.00160.36030.02120.278315.1593-10.02896.2796
41.11210.15620.68010.87840.69593.21130.0865-0.0248-0.0113-0.0731-0.0063-0.027-0.04660.0239-0.07330.1350.02550.030.12030.00960.21217.8689-1.457839.6619
53.42020.77872.31110.44420.64242.35710.1282-0.1591-0.1509-0.0166-0.0352-0.15980.05030.2064-0.09770.18460.00290.02980.23410.00140.242120.70751.657650.3472
62.91270.02541.34150.78440.17082.29920.0588-0.26150.13950.051-0.064-0.0596-0.05860.0621-0.00260.1578-0.00920.03710.163-0.01450.20214.88114.714153.2804
73.49012.5020.2585.6657-1.60271.75540.1492-0.02120.34790.0018-0.1365-0.0327-0.09950.0101-0.01480.15720.02990.04330.1552-0.00540.2299-10.470517.5497-33.4169
81.17880.3561-0.4622.9217-2.19115.4638-0.0346-0.01470.0662-0.2870.1978-0.02950.1706-0.0478-0.14320.11390.02980.01130.1366-0.02670.2315-14.242911.4187-32.156
90.09970.50490.5559-0.1192-0.00183.18150.11330.1146-0.06370.08390.123-0.0680.07720.4026-0.18640.33130.1732-0.0230.3712-0.04810.287-10.70623.55173.8286
109.4331-0.2521-1.14650.05230.36452.69740.43590.6652-0.31230.0812-0.1981-0.00220.2793-0.4267-0.22210.44040.1151-0.10060.3766-0.03390.2295-24.3830.154613.439
114.20430.88890.31066.57014.09984.37130.4906-0.0208-1.24470.0673-0.24260.59480.6252-0.219-0.16310.47090.0358-0.22290.4109-0.05130.7342-32.7506-8.460317.2861
122.95680.8648-1.07441.88461.03883.65520.27390.0502-0.1541-0.109-0.18940.21480.1964-0.1601-0.07860.31320.0887-0.10460.2468-0.01720.2607-20.41381.321321.8823
130.9698-0.45470.1350.73820.03770.04510.36350.4801-0.4684-0.069-0.0822-0.28550.44530.33390.20790.53640.7569-0.210.3918-0.18930.3802-7.3084-6.98376.1531
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 58 through 79 )A58 - 79
2X-RAY DIFFRACTION2chain 'A' and (resid 80 through 110 )A80 - 110
3X-RAY DIFFRACTION3chain 'A' and (resid 111 through 157 )A111 - 157
4X-RAY DIFFRACTION4chain 'A' and (resid 158 through 289 )A158 - 289
5X-RAY DIFFRACTION5chain 'A' and (resid 290 through 308 )A290 - 308
6X-RAY DIFFRACTION6chain 'A' and (resid 309 through 407 )A309 - 407
7X-RAY DIFFRACTION7chain 'B' and (resid 58 through 122 )B58 - 122
8X-RAY DIFFRACTION8chain 'B' and (resid 123 through 157 )B123 - 157
9X-RAY DIFFRACTION9chain 'B' and (resid 158 through 289 )B158 - 289
10X-RAY DIFFRACTION10chain 'B' and (resid 290 through 308 )B290 - 308
11X-RAY DIFFRACTION11chain 'B' and (resid 309 through 323 )B309 - 323
12X-RAY DIFFRACTION12chain 'B' and (resid 324 through 378 )B324 - 378
13X-RAY DIFFRACTION13chain 'B' and (resid 379 through 407 )B379 - 407

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