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- PDB-5k69: Crystal structure of Mycobacterium tuberculosis L,D-transpeptidas... -

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Basic information

Entry
Database: PDB / ID: 5k69
TitleCrystal structure of Mycobacterium tuberculosis L,D-transpeptidase 2 with carbapenem drug T224
ComponentsL,D-transpeptidase 2
KeywordsTRANSFERASE/TRANSFERASE INHIBITOR / peptidase / IgD_like domain / YkuD domain / TRANSFERASE-TRANSFERASE INHIBITOR complex
Function / homology
Function and homology information


peptidoglycan-protein cross-linking / peptidoglycan L,D-transpeptidase activity / Transferases; Acyltransferases; Aminoacyltransferases / acyltransferase activity / cell wall organization / regulation of cell shape / metal ion binding / plasma membrane
Similarity search - Function
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 ...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-6QR / L,D-transpeptidase 2
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.001 Å
AuthorsLamichhane, G. / Ginell, S.L. / Kumar, P.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)1R21AI111739-01 United States
National Institutes of Health/Office of the Director1DP2OD008459-01 United States
CitationJournal: Nat. Chem. Biol. / Year: 2017
Title: Non-classical transpeptidases yield insight into new antibacterials.
Authors: Kumar, P. / Kaushik, A. / Lloyd, E.P. / Li, S.G. / Mattoo, R. / Ammerman, N.C. / Bell, D.T. / Perryman, A.L. / Zandi, T.A. / Ekins, S. / Ginell, S.L. / Townsend, C.A. / Freundlich, J.S. / Lamichhane, G.
History
DepositionMay 24, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 9, 2016Provider: repository / Type: Initial release
Revision 1.1Nov 23, 2016Group: Database references
Revision 1.2Dec 28, 2016Group: Database references
Revision 1.3Sep 20, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Dec 11, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5Sep 27, 2023Group: Advisory / Data collection ...Advisory / Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_unobs_or_zero_occ_atoms
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.6Nov 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)87,8137
Polymers86,8152
Non-polymers9975
Water5,116284
1
A: L,D-transpeptidase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,9524
Polymers43,4081
Non-polymers5453
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: L,D-transpeptidase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,8603
Polymers43,4081
Non-polymers4532
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
A: L,D-transpeptidase 2
hetero molecules

B: L,D-transpeptidase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)87,8137
Polymers86,8152
Non-polymers9975
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_648-x+1,y-1/2,-z+31
Buried area2560 Å2
ΔGint-15 kcal/mol
Surface area30360 Å2
MethodPISA
Unit cell
Length a, b, c (Å)61.140, 94.150, 75.630
Angle α, β, γ (deg.)90.00, 93.20, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 43407.711 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv) (bacteria)
Strain: ATCC 25618 / H37Rv / Gene: ldtB, lppS, Rv2518c, RVBD_2518c, P425_02624 / Plasmid: pET38a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: I6Y9J2, Transferases; Acyltransferases; Aminoacyltransferases
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-6QR / (2~{S},3~{R},4~{R})-4-(1~{H}-indol-3-ylsulfanyl)-3-methyl-2-[(2~{S},3~{S})-3-oxidanyl-1-oxidanylidene-butan-2-yl]-3,4-dihydro-2~{H}-pyrrole-5-carboxylic acid


Mass: 360.427 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C18H20N2O4S
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 284 / 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 / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.5 Å3/Da / Density % sol: 50.87 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8 / Details: PEG5000MME, Ammonium sulfate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 4, 2015
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 2→28.98 Å / Num. obs: 70044 / % possible obs: 97.8 % / Redundancy: 3.4 % / CC1/2: 0.899 / Rmerge(I) obs: 0.073 / Rsym value: 0.066 / Net I/σ(I): 14.42
Reflection shellResolution: 2→2.03 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.474 / Mean I/σ(I) obs: 2.63 / % possible all: 96.9

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-3000data reduction
HKL-3000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5DU7

5du7


Resolution: 2.001→28.98 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 25.25 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2293 2506 3.58 %Random selection
Rwork0.1936 ---
obs0.1949 70044 61.67 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.001→28.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5275 0 68 284 5627
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0045478
X-RAY DIFFRACTIONf_angle_d0.8647500
X-RAY DIFFRACTIONf_dihedral_angle_d11.4071895
X-RAY DIFFRACTIONf_chiral_restr0.033839
X-RAY DIFFRACTIONf_plane_restr0.004981
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.001-2.03950.2731940.23312535X-RAY DIFFRACTION42
2.0395-2.08110.27481010.22562904X-RAY DIFFRACTION47
2.0811-2.12630.24131230.22322921X-RAY DIFFRACTION49
2.1263-2.17580.24591020.22032970X-RAY DIFFRACTION49
2.1758-2.23020.29151120.22633004X-RAY DIFFRACTION49
2.2302-2.29050.30071110.22352991X-RAY DIFFRACTION49
2.2905-2.35780.26651120.22683013X-RAY DIFFRACTION50
2.3578-2.43390.23461130.23343047X-RAY DIFFRACTION50
2.4339-2.52080.2571220.22783120X-RAY DIFFRACTION51
2.5208-2.62170.28741210.23573248X-RAY DIFFRACTION53
2.6217-2.74090.27361310.22473625X-RAY DIFFRACTION60
2.7409-2.88530.24941500.21984004X-RAY DIFFRACTION66
2.8853-3.06590.26031500.22054391X-RAY DIFFRACTION72
3.0659-3.30230.21661710.2044689X-RAY DIFFRACTION77
3.3023-3.63410.23821890.18874920X-RAY DIFFRACTION81
3.6341-4.15860.23561980.17335184X-RAY DIFFRACTION85
4.1586-5.23440.19111980.15295321X-RAY DIFFRACTION88
5.2344-28.98310.16792080.16865651X-RAY DIFFRACTION93

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