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- PDB-4zfq: Structure of M. tuberculosis (3,3) L,D-Transpeptidase, LdtMt5. (M... -

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Basic information

Entry
Database: PDB / ID: 4zfq
TitleStructure of M. tuberculosis (3,3) L,D-Transpeptidase, LdtMt5. (Meropenen-adduct form)
ComponentsL,D-transpeptidase 5
KeywordsTRANSFERASE / peptidoglycan linkage / cell wall biosynthesis / carbapenems / Mycobaterium tuberculosis / L.D-transpeptidases
Function / homology
Function and homology information


Transferases; Acyltransferases; Aminoacyltransferases / acyltransferase activity / peptidoglycan biosynthetic process / cell wall organization / regulation of cell shape
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 / Immunoglobulin-like / Beta Barrel / Sandwich / Mainly Beta
Similarity search - Domain/homology
Chem-DWZ / DI(HYDROXYETHYL)ETHER / L,D-transpeptidase 5
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.799 Å
AuthorsBasta, L. / Ghosh, A. / Lamichhane, G. / Bianchet, M.A.
Citation
Journal: J.Biol.Chem. / Year: 2015
Title: Loss of a Functionally and Structurally Distinct ld-Transpeptidase, LdtMt5, Compromises Cell Wall Integrity in Mycobacterium tuberculosis.
Authors: Brammer Basta, L.A. / Ghosh, A. / Pan, Y. / Jakoncic, J. / Lloyd, E.P. / Townsend, C.A. / Lamichhane, G. / Bianchet, M.A.
#1: Journal: Structure / Year: 2012
Title: Targeting the cell wall of Mycobacterium tuberculosis: structure and mechanism of L,D-transpeptidase 2.
Authors: Erdemli, S.B. / Gupta, R. / Bishai, W.R. / Lamichhane, G. / Amzel, L.M. / Bianchet, M.A.
History
DepositionApr 21, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 2, 2015Provider: repository / Type: Initial release
Revision 1.1Sep 9, 2015Group: Database references
Revision 1.2Oct 28, 2015Group: Database references
Revision 1.3Feb 2, 2022Group: Database references / Derived calculations / Structure summary
Category: chem_comp / citation ...chem_comp / citation / database_2 / entity / pdbx_entity_nonpoly / pdbx_struct_oper_list / struct_conn
Item: _chem_comp.name / _chem_comp.pdbx_synonyms ..._chem_comp.name / _chem_comp.pdbx_synonyms / _citation.journal_id_CSD / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _pdbx_struct_oper_list.symmetry_operation / _struct_conn.pdbx_leaving_atom_flag
Revision 1.4Sep 27, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.5Oct 23, 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 5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,5304
Polymers47,9331
Non-polymers5983
Water77543
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)99.393, 99.393, 193.384
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number180
Space group name H-MP6222

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Components

#1: Protein L,D-transpeptidase 5 / LDT 5 / Ldt(Mt5)


Mass: 47932.512 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (strain CDC 1551 / Oshkosh) (bacteria)
Strain: CDC 1551 / Oshkosh / Gene: MT0501 / Production host: Escherichia coli (E. coli)
References: UniProt: P9WKV2, Transferases; Acyltransferases; Aminoacyltransferases
#2: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#3: Chemical ChemComp-DWZ / (2S,3R,4S)-4-{[(3S,5S)-5-(dimethylcarbamoyl)pyrrolidin-3-yl]sulfanyl}-2-[(2S,3R)-3-hydroxy-1-oxobutan-2-yl]-3-methyl-3,4-dihydro-2H-pyrrole-5-carboxylic acid / Meropenem, bound form


Mass: 385.478 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H27N3O5S / Comment: antibiotic*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 43 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.88 Å3/Da / Density % sol: 57.24 %
Crystal growTemperature: 293.5 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: 85 mM sodium citrate, pH 5.6, 25.5% PEG 4,000, 170 mM ammonium acetate, and 15% glycerol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X6A / Wavelength: 1.116 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 1, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.116 Å / Relative weight: 1
ReflectionResolution: 2.799→30 Å / Num. obs: 14630 / % possible obs: 100 % / Redundancy: 22.4 % / Rsym value: 0.053 / Net I/σ(I): 53.3
Reflection shellResolution: 2.8→2.85 Å / Rmerge(I) obs: 0.49 / Mean I/σ(I) obs: 6.3 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-2000data reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4Z7A

4z7a


Resolution: 2.799→29.044 Å / SU ML: 0.33 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 30.87 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2766 734 5.07 %
Rwork0.2301 --
obs0.2324 14486 99.19 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.799→29.044 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2645 0 30 43 2718
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.012759
X-RAY DIFFRACTIONf_angle_d1.2463776
X-RAY DIFFRACTIONf_dihedral_angle_d14.249965
X-RAY DIFFRACTIONf_chiral_restr0.047414
X-RAY DIFFRACTIONf_plane_restr0.005495
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7991-3.0150.37591510.27492663X-RAY DIFFRACTION99
3.015-3.3180.3251440.27562696X-RAY DIFFRACTION100
3.318-3.79730.32361380.23912700X-RAY DIFFRACTION99
3.7973-4.78070.23911370.20982754X-RAY DIFFRACTION99
4.7807-29.0460.24851640.21832939X-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)
11.1651-0.48661.39413.1548-0.97084.26630.00410.7125-0.0125-0.6216-0.0051-0.02070.84260.6072-0.00011.01420.1576-0.13820.85230.10440.6675-32.3638-27.6028-6.6527
23.0977-1.16310.72613.223-1.55082.76560.04180.0999-0.23840.2679-0.7296-0.67170.48591.3518-0.04510.6084-0.072-0.01740.83160.32310.7941-31.1163-3.3328-35.2759
34.44131.3174-1.32524.6369-0.97473.38990.4047-0.1340.47280.369-0.6-0.2655-0.83190.8302-0.0450.6936-0.29350.00160.66440.14270.7156-36.088519.1743-47.1985
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and ((resseq 63:154))
2X-RAY DIFFRACTION2chain 'A' and ((resseq 157:262) or (resseq 394:416))
3X-RAY DIFFRACTION3chain 'A' and ((resseq 263:393))

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