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

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Basic information

Entry
Database: PDB / ID: 8aho
TitleCrystal structure of the transpeptidase LdtMt2 from Mycobacterium tuberculosis in complex with cyanamide analogue 31
ComponentsTranspeptidase,Lipoprotein LppS
KeywordsANTIMICROBIAL PROTEIN / L / D-transpeptidase / LdtMt2 / Inhibitor / Covalent
Function / homologyNITRATE ION / : / :
Function and homology information
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
DepositionJul 22, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 2, 2023Provider: repository / Type: Initial release
Revision 1.1Oct 16, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / 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: Transpeptidase,Lipoprotein LppS
B: Transpeptidase,Lipoprotein LppS
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,77913
Polymers76,1042
Non-polymers67411
Water7,080393
1
A: Transpeptidase,Lipoprotein LppS
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,2935
Polymers38,0521
Non-polymers2414
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Transpeptidase,Lipoprotein LppS
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,4858
Polymers38,0521
Non-polymers4337
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)61.250, 94.261, 75.667
Angle α, β, γ (deg.)90.000, 92.690, 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 Transpeptidase,Lipoprotein LppS


Mass: 38052.172 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Gene: lppS, MTR2092_25980, lppS, ERS007683_02655 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A8D5X3I3, UniProt: A0A655I6I1

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Non-polymers , 5 types, 404 molecules

#2: Chemical ChemComp-NO3 / NITRATE ION


Mass: 62.005 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: NO3
#3: Chemical
ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#4: Chemical ChemComp-NA / SODIUM ION


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


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 393 / 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: 57.26 %
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→61.18 Å / Num. obs: 74669 / % possible obs: 99.79 % / Redundancy: 6.9 % / CC1/2: 0.89 / Rmerge(I) obs: 0.136 / Rpim(I) all: 0.057 / Rrim(I) all: 0.147 / Net I/σ(I): 8.9
Reflection shell

Diffraction-ID: 1

Resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
2.3-2.340.7821.318650.8650.3190.84698.36
6.23-61.20.04626.519650.9970.0190.05100

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation6.18 Å61.18 Å

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Processing

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

6rrm


Resolution: 2.3→61.18 Å / SU ML: 0.32 / Cross valid method: THROUGHOUT / σ(F): 1.38 / Phase error: 28.29 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.248 3867 5.18 %
Rwork0.2087 70802 -
obs0.2108 74669 99.41 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 124.96 Å2 / Biso mean: 45.3178 Å2 / Biso min: 23.25 Å2
Refinement stepCycle: final / Resolution: 2.3→61.18 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5209 0 41 393 5643
Biso mean--66.22 44.4 -
Num. residues----699
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 28

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.3-2.330.3251150.2982439255496
2.33-2.360.32431610.285625982759100
2.36-2.390.32011570.299424752632100
2.39-2.420.33531350.270125172652100
2.42-2.460.2741140.280325812695100
2.46-2.490.2981570.268825222679100
2.49-2.530.28891410.271925502691100
2.53-2.570.31311260.250525232649100
2.57-2.620.35271520.258325652717100
2.62-2.660.32631260.294425152641100
2.67-2.720.31411360.291725192655100
2.72-2.770.25951290.250125682697100
2.77-2.830.31931590.251525092668100
2.83-2.90.33181230.240625442667100
2.9-2.970.28521420.227625802722100
2.97-3.050.30031520.224225412693100
3.05-3.140.29631210.219425382659100
3.14-3.240.27731340.203725352669100
3.24-3.360.2591380.213225622700100
3.36-3.490.25841290.20725252654100
3.49-3.650.24241500.20842485263598
3.65-3.840.27341310.21982474260597
3.84-4.080.26391480.19352441258997
4.08-4.40.14631380.142425502688100
4.4-4.840.18041460.138625322678100
4.84-5.540.17071360.155825592695100
5.54-6.980.20981350.17925422677100
6.98-61.180.20471360.1982513264999
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)
10.3245-0.0054-0.90550.38510.6573.52740.02080.10710.0282-0.07360.06770.0048-0.18590.0174-0.08470.30740.0521-0.02490.34450.00520.315310.5139-103.011417.5027
22.5111-0.22350.23361.5568-0.37242.27980.0935-0.40010.15840.0633-0.1688-0.1384-0.19850.08660.0710.3473-0.02820.00480.30370.01220.287413.43-91.963254.4187
31.0416-0.07681.58434.1597-0.4882.5423-0.0418-0.00730.1717-0.0221-0.0287-0.1183-0.15420.13830.02210.2827-0.02030.04170.28870.01410.3344-9.2234-77.4067-34.9629
40.8185-0.03570.16812.499-1.43483.3139-0.0252-0.2970.0376-0.13740.03340.1718-0.0716-0.08980.00440.2496-0.0233-0.00510.3973-0.02890.2872-14.4713-83.0338-30.3363
50.62760.42140.20930.28450.2052.4134-0.00470.0374-0.00130.1880.1284-0.0712-0.11390.0751-0.11460.37190.1519-0.01790.4271-0.02910.3171-10.0015-90.90130.6557
62.0867-0.342-0.19441.72720.791.56130.2260.0759-0.26210.1586-0.21020.08830.344-0.1826-0.03410.48910.0529-0.07610.4226-0.0070.3018-19.0385-97.509817.4855
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 59 through 248 )A59 - 248
2X-RAY DIFFRACTION2chain 'A' and (resid 249 through 407 )A249 - 407
3X-RAY DIFFRACTION3chain 'B' and (resid 58 through 110 )B58 - 110
4X-RAY DIFFRACTION4chain 'B' and (resid 111 through 157 )B111 - 157
5X-RAY DIFFRACTION5chain 'B' and (resid 158 through 270 )B158 - 270
6X-RAY DIFFRACTION6chain 'B' and (resid 271 through 407 )B271 - 407

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