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- PDB-6rrm: Crystal structure of LdtMt2 from Mycobacterium tuberculosis bound... -

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Basic information

Entry
Database: PDB / ID: 6rrm
TitleCrystal structure of LdtMt2 from Mycobacterium tuberculosis bound to Ebselen
ComponentsL,D-transpeptidase 2
KeywordsANTIMICROBIAL PROTEIN / beta lactmase / antibiotic resistance / tuberculosis
Function / homology
Function and homology information


peptidoglycan-based cell wall biogenesis / peptidoglycan L,D-transpeptidase activity / peptidoglycan metabolic process / Transferases; Acyltransferases; Aminoacyltransferases / acyltransferase activity / peptidoglycan biosynthetic process / peptidoglycan-based cell wall / cell wall organization / regulation of cell shape / metal ion binding / plasma membrane
Similarity search - Function
Immunoglobulin-like - #3710 / L,D-transpeptidase catalytic domain-like / L,D-transpeptidase catalytic domain-like / 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 ...Immunoglobulin-like - #3710 / L,D-transpeptidase catalytic domain-like / L,D-transpeptidase catalytic domain-like / 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. / Immunoglobulin-like / Beta Barrel / Sandwich / Mainly Beta
Similarity search - Domain/homology
N-phenyl-2-selanylbenzamide / AMMONIUM ION / L,D-transpeptidase 2
Similarity search - Component
Biological speciesMycobacterium tuberculosis CDC1551 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.64 Å
AuthorsBrem, J. / Lohans, C. / Schofield, C.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Medical Research Council (United Kingdom) United Kingdom
CitationJournal: Chem.Commun.(Camb.) / Year: 2019
Title: Targeting the Mycobacterium tuberculosis transpeptidase LdtMt2with cysteine-reactive inhibitors including ebselen.
Authors: de Munnik, M. / Lohans, C.T. / Lang, P.A. / Langley, G.W. / Malla, T.R. / Tumber, A. / Schofield, C.J. / Brem, J.
History
DepositionMay 20, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 14, 2019Provider: repository / Type: Initial release
Revision 1.1Aug 21, 2019Group: Data collection / Derived calculations
Category: pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop
Revision 1.2Sep 4, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.3Apr 12, 2023Group: Database references / Derived calculations / Structure summary
Category: chem_comp / database_2 ...chem_comp / database_2 / entity / pdbx_entity_nonpoly
Item: _chem_comp.name / _chem_comp.pdbx_synonyms ..._chem_comp.name / _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity.pdbx_description / _pdbx_entity_nonpoly.name
Revision 1.4Feb 7, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.5Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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)76,84710
Polymers76,0242
Non-polymers8238
Water9,584532
1
A: L,D-transpeptidase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,4175
Polymers38,0121
Non-polymers4044
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: L,D-transpeptidase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,4315
Polymers38,0121
Non-polymers4184
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)61.220, 93.570, 75.490
Angle α, β, γ (deg.)90.000, 93.010, 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: 38012.211 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis CDC1551 (bacteria)
Gene: ldtB, MT2594, V735_02606 / Variant: CDC 1551 / Oshkosh / Production host: Escherichia coli (E. coli)
References: UniProt: O53223, Transferases; Acyltransferases; Aminoacyltransferases

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Non-polymers , 5 types, 540 molecules

#2: Chemical ChemComp-NH4 / AMMONIUM ION


Mass: 18.038 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: H4N
#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-9JT / N-phenyl-2-selanylbenzamide / ~{N}-phenyl-2-selanyl-benzamide / Ebselen, bound form


Mass: 276.193 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C13H11NOSe / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


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


Mass: 18.015 Da / Num. of mol.: 532 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 57.15 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6.3 / Details: 0.2 M Ammonium nitrate pH 6.3, 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: 0.97625 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Aug 2, 2018
RadiationMonochromator: Double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97625 Å / Relative weight: 1
ReflectionResolution: 1.64→58.7 Å / Num. obs: 103762 / % possible obs: 99.9 % / Redundancy: 6.7 % / Biso Wilson estimate: 27.2 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.07 / Rpim(I) all: 0.029 / Rrim(I) all: 0.076 / Net I/σ(I): 12.1 / Num. measured all: 690195 / Scaling rejects: 30
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
1.64-1.686.81.5635170576190.570.6431.6921.1100
7.33-58.76.60.043801212150.9980.0190.04734.699.6

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation4.55 Å61.03 Å
Translation4.55 Å61.03 Å

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Processing

Software
NameVersionClassificationNB
XDSdata reduction
Aimless0.7.1data scaling
PHASER2.7.16phasing
PHENIX1.11.1_2575refinement
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5DUJ

5duj


Resolution: 1.64→48.753 Å / SU ML: 0.27 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 28.79
RfactorNum. reflection% reflection
Rfree0.223 5088 4.91 %
Rwork0.2001 --
obs0.2012 103680 99.84 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 136.24 Å2 / Biso mean: 37.4962 Å2 / Biso min: 17.57 Å2
Refinement stepCycle: final / Resolution: 1.64→48.753 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5222 0 65 538 5825
Biso mean--50.68 42.45 -
Num. residues----702
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0065552
X-RAY DIFFRACTIONf_angle_d0.817622
X-RAY DIFFRACTIONf_chiral_restr0.057843
X-RAY DIFFRACTIONf_plane_restr0.0051010
X-RAY DIFFRACTIONf_dihedral_angle_d12.9623177
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.64-1.65870.42141690.397232453414100
1.6587-1.67820.39371590.381632813440100
1.6782-1.69860.3561750.3632863461100
1.6986-1.72010.4161630.350933133476100
1.7201-1.74280.35351560.325132683424100
1.7428-1.76660.32541580.301432553413100
1.7666-1.79190.32171770.285733043481100
1.7919-1.81860.33271740.275632683442100
1.8186-1.84710.31081630.26333083471100
1.8471-1.87730.31861690.248632693438100
1.8773-1.90970.29331580.237832893447100
1.9097-1.94440.29421570.236332693426100
1.9444-1.98180.25571670.21533223489100
1.9818-2.02230.24121610.217532343395100
2.0223-2.06630.25891880.220332903478100
2.0663-2.11430.26921790.212132983477100
2.1143-2.16720.24631950.203632403435100
2.1672-2.22580.24131690.196433033472100
2.2258-2.29130.21821630.199732773440100
2.2913-2.36530.25061730.18932693442100
2.3653-2.44980.23521800.195932983478100
2.4498-2.54790.23371630.189632883451100
2.5479-2.66380.22131690.197532853454100
2.6638-2.80420.25781830.208132793462100
2.8042-2.97990.24011790.208732443423100
2.9799-3.210.23761630.197333083471100
3.21-3.53290.20131640.191433043468100
3.5329-4.04390.18451870.17543294348199
4.0439-5.0940.1571770.150333103487100
5.094-48.77420.17421500.186933943544100
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)
12.3982-0.64961.12941.4333-0.28572.59080.0405-0.21920.24290.0574-0.1116-0.1919-0.21660.0960.05060.2272-0.03830.00980.20540.00740.229813.4339-91.434854.5638
20.0210.0292-0.24290.6688-0.89063.02360.0176-0.08990.04660.09020.0632-0.0494-0.03990.1798-0.08820.21650.04020.00210.3447-0.02260.2804-11.2902-87.3982-11.5905
36.9434-0.4584-0.65351.74530.9254.29240.49150.2078-0.78760.109-0.07290.39940.5852-0.3267-0.0120.46580.121-0.15920.4022-0.00740.2958-27.8092-99.823914.9677
41.5274-0.2358-0.4060.97040.3413.22390.21260.0495-0.25140.0602-0.1035-0.00860.34050.0962-0.14380.37330.0783-0.05990.2937-0.02380.2606-17.6931-97.130116.8762
50.00680.1626-0.37010.24941.36374.28890.02670.15470.0036-0.07320.0947-0.0465-0.01260.4353-0.11390.25990.0894-0.00380.36620.0310.253510.3521-102.743217.2768
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 249 through 407 )A249 - 407
2X-RAY DIFFRACTION2chain 'B' and (resid 57 through 289 )B57 - 289
3X-RAY DIFFRACTION3chain 'B' and (resid 290 through 318 )B290 - 318
4X-RAY DIFFRACTION4chain 'B' and (resid 319 through 407 )B319 - 407
5X-RAY DIFFRACTION5chain 'A' and (resid 57 through 248 )A57 - 248

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