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

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Basic information

Entry
Database: PDB / ID: 8pxz
TitleCrystal structure of the transpeptidase LdtMt2 from Mycobacterium tuberculosis in complex with natural substrate
Components
  • (Peptidoglycan ...) x 2
  • L,D-transpeptidase 2
KeywordsANTIMICROBIAL PROTEIN / LdtMt2 / Substrate complex / Mycobacterium tuberculosis / L / D-transpeptidase
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
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 / L,D-transpeptidase catalytic domain-like / Prokaryotic membrane lipoprotein lipid attachment site profile.
Similarity search - Domain/homology
D-ALANINE / polypeptide(D) / L,D-transpeptidase 2
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
Corynebacterium jeikeium (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.98 Å
Authorsde Munnik, M. / Schofield, C.J.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research Council (BBSRC) United Kingdom
CitationJournal: Commun Biol / Year: 2024
Title: Biochemical and crystallographic studies of L,D-transpeptidase 2 from Mycobacterium tuberculosis with its natural monomer substrate.
Authors: de Munnik, M. / Lang, P.A. / Calvopina, K. / Rabe, P. / Brem, J. / Schofield, C.J.
History
DepositionJul 24, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 7, 2024Provider: repository / Type: Initial release
Revision 2.0Oct 16, 2024Group: Advisory / Atomic model ...Advisory / Atomic model / Author supporting evidence / Data collection / Database references / Derived calculations / Non-polymer description / Polymer sequence / Source and taxonomy / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp / chem_comp_atom / chem_comp_bond / citation / citation_author / entity / entity_poly / entity_poly_seq / entity_src_nat / pdbx_distant_solvent_atoms / pdbx_entity_instance_feature / pdbx_entity_nonpoly / pdbx_entry_details / pdbx_modification_feature / pdbx_nonpoly_scheme / pdbx_poly_seq_scheme / pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / pdbx_validate_main_chain_plane / pdbx_validate_peptide_omega / pdbx_validate_rmsd_angle / pdbx_validate_torsion / struct_asym / struct_conn / struct_mon_prot_cis / struct_ref / struct_ref_seq
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.label_seq_id / _atom_site.pdbx_formal_charge / _atom_site.type_symbol / _atom_site_anisotrop.U[1][1] / _atom_site_anisotrop.U[1][2] / _atom_site_anisotrop.U[1][3] / _atom_site_anisotrop.U[2][2] / _atom_site_anisotrop.U[2][3] / _atom_site_anisotrop.U[3][3] / _atom_site_anisotrop.id / _atom_site_anisotrop.pdbx_auth_asym_id / _atom_site_anisotrop.pdbx_auth_atom_id / _atom_site_anisotrop.pdbx_auth_comp_id / _atom_site_anisotrop.pdbx_auth_seq_id / _atom_site_anisotrop.pdbx_label_asym_id / _atom_site_anisotrop.pdbx_label_atom_id / _atom_site_anisotrop.pdbx_label_comp_id / _atom_site_anisotrop.pdbx_label_seq_id / _atom_site_anisotrop.type_symbol / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.pdbx_synonyms / _chem_comp.type / _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 / _entity.formula_weight / _entity.pdbx_description / _entity.src_method / _entity.type / _pdbx_distant_solvent_atoms.auth_seq_id / _pdbx_entry_details.has_protein_modification / _pdbx_struct_assembly.oligomeric_count / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_assembly_gen.asym_id_list

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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: Peptidoglycan tripeptide
C: Peptidoglycan dipeptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,9026
Polymers38,7153
Non-polymers1873
Water6,341352
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: mass spectrometry
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)77.120, 95.830, 59.230
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

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Protein , 1 types, 1 molecules A

#1: Protein L,D-transpeptidase 2 / LDT 2 / Ldt(Mt2)


Mass: 38009.145 Da / Num. of mol.: 1
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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Peptidoglycan ... , 2 types, 2 molecules BC

#2: Polypeptide(D) Peptidoglycan tripeptide


Mass: 388.419 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Corynebacterium jeikeium (bacteria)
#3: Protein/peptide Peptidoglycan dipeptide


Mass: 317.341 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Corynebacterium jeikeium (bacteria)

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Non-polymers , 4 types, 355 molecules

#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-DAL / D-ALANINE


Type: D-peptide linking / Mass: 89.093 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H7NO2 / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: Cl
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 352 / 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: 57.28 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 0.1 M HEPES pH 7.0, 25% Jeffamine ED-2001 pH 7.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.97628 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Aug 4, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97628 Å / Relative weight: 1
ReflectionResolution: 1.98→42.18 Å / Num. obs: 31119 / % possible obs: 99.5 % / Redundancy: 13.2 % / Biso Wilson estimate: 31.85 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.14 / Rpim(I) all: 0.038 / Rrim(I) all: 0.14 / Net I/σ(I): 12.3
Reflection shellResolution: 1.98→2.01 Å / Redundancy: 12.1 % / Rmerge(I) obs: 1.997 / Mean I/σ(I) obs: 1.4 / Num. unique obs: 1348 / CC1/2: 0.536 / Rpim(I) all: 0.606 / Rrim(I) all: 2.091 / % possible all: 89.3

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Processing

Software
NameVersionClassification
PHENIX(1.18.2_3874: ???)refinement
xia2data scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.98→42.18 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 25.13 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2255 1488 4.79 %
Rwork0.1799 --
obs0.182 31060 99.42 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.98→42.18 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2629 0 59 352 3040
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.012783
X-RAY DIFFRACTIONf_angle_d1.1323817
X-RAY DIFFRACTIONf_dihedral_angle_d12.156957
X-RAY DIFFRACTIONf_chiral_restr0.06427
X-RAY DIFFRACTIONf_plane_restr0.007509
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.98-2.040.33481170.27722489X-RAY DIFFRACTION94
2.04-2.120.27211420.23462642X-RAY DIFFRACTION100
2.12-2.20.27781420.21272665X-RAY DIFFRACTION100
2.2-2.30.2591210.19672669X-RAY DIFFRACTION100
2.3-2.420.24911220.19872690X-RAY DIFFRACTION100
2.42-2.580.24411340.19172700X-RAY DIFFRACTION100
2.58-2.770.25311250.18822680X-RAY DIFFRACTION100
2.77-3.050.2251380.18112701X-RAY DIFFRACTION100
3.05-3.490.23061400.17472727X-RAY DIFFRACTION100
3.5-4.40.1891590.15462727X-RAY DIFFRACTION100
4.4-42.180.21161480.17072882X-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)
12.685-0.17980.52492.8481-2.0716.8687-0.09150.005-0.09170.53970.06360.57290.1584-0.3626-0.07290.2845-0.03330.10010.2513-0.05280.4016-18.272812.118821.2851
25.3833.8114-3.44084.6235-5.45936.99120.07530.1336-0.12960.158-0.12850.00280.21560.2017-0.03380.378-0.01330.03630.2571-0.0480.3166-15.83824.93915.9721
32.71670.27140.63230.8479-0.01730.7072-0.02390.1704-0.01060.20.00470.0349-0.03340.0040.01770.328-0.01740.01370.2736-0.00750.187612.569319.140319.8686
42.3332-0.0629-0.53890.9106-0.05491.28020.07940.21630.09680.1154-0.1209-0.2009-0.15090.17860.03030.3192-0.0191-0.09160.32710.0350.287435.175527.975114.1049
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 57 through 79 )
2X-RAY DIFFRACTION2chain 'A' and (resid 80 through 131 )
3X-RAY DIFFRACTION3chain 'A' and (resid 132 through 270 )
4X-RAY DIFFRACTION4chain 'A' and (resid 271 through 407 )

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