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- PDB-5duj: Crystal structure of ldtMt2 in complex with Faropenem adduct -

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Basic information

Entry
Database: PDB / ID: 5duj
TitleCrystal structure of ldtMt2 in complex with Faropenem adduct
ComponentsL,D-transpeptidase 2
KeywordsTRANSFERASE / LD-TRANSPEPTIDASE / Peptidoglycan synthesis enzyme / cell wall enzyme
Function / homology
Function and homology information


peptidoglycan-based cell wall biogenesis / peptidoglycan-protein cross-linking / peptidoglycan metabolic process / peptidoglycan L,D-transpeptidase activity / Transferases; Acyltransferases; Aminoacyltransferases / acyltransferase activity / peptidoglycan-based cell wall / cell wall organization / regulation of cell shape / extracellular region ...peptidoglycan-based cell wall biogenesis / peptidoglycan-protein cross-linking / peptidoglycan metabolic process / peptidoglycan L,D-transpeptidase activity / Transferases; Acyltransferases; Aminoacyltransferases / acyltransferase activity / peptidoglycan-based cell wall / cell wall organization / regulation of cell shape / extracellular region / 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
BETA-MERCAPTOETHANOL / Chem-DGF / L,D-transpeptidase 2 / L,D-transpeptidase 2
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.17 Å
AuthorsKumar, P. / Lamichhane, G.
Funding support United States, 1items
OrganizationGrant numberCountry
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
DepositionSep 18, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 28, 2016Provider: repository / Type: Initial release
Revision 1.1Nov 9, 2016Group: Database references
Revision 1.2Nov 23, 2016Group: Database references
Revision 1.3Dec 28, 2016Group: Database references
Revision 1.4Sep 20, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5Sep 27, 2023Group: 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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)79,8917
Polymers79,0642
Non-polymers8275
Water8,323462
1
A: L,D-transpeptidase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,9944
Polymers39,5321
Non-polymers4623
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: L,D-transpeptidase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,8973
Polymers39,5321
Non-polymers3652
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)79,8917
Polymers79,0642
Non-polymers8275
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_546-x,y-1/2,-z+11
Buried area2610 Å2
ΔGint-26 kcal/mol
Surface area30760 Å2
MethodPISA
Unit cell
Length a, b, c (Å)61.051, 93.929, 75.215
Angle α, β, γ (deg.)90.00, 92.72, 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: 39532.004 Da / Num. of mol.: 2 / Fragment: residues 42-408
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Strain: CDC 1551 / Oshkosh / Gene: ldtB, MT2594, V735_02606 / Plasmid: pET28a / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 (DE3)
References: UniProt: O53223, UniProt: I6Y9J2*PLUS, Transferases; Acyltransferases; Aminoacyltransferases
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-BME / BETA-MERCAPTOETHANOL


Mass: 78.133 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6OS
#4: Chemical ChemComp-DGF / (2R,5R)-2-[(2S,3R)-3-hydroxy-1-oxobutan-2-yl]-5-[(2R)-tetrahydrofuran-2-yl]-2,5-dihydro-1,3-thiazole-4-carboxylic acid / FAROPENEM PRODUCT, BOUND FORM


Mass: 287.332 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C12H17NO5S
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 462 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.87 Å3/Da / Density % sol: 57.12 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / Details: 20% 5000MME, 200mM ammonium sulfate / PH range: 7.0-8.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.54 Å
DetectorType: RIGAKU SATURN 944+ / Detector: CCD / Date: Oct 7, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.17→50 Å / Num. obs: 42667 / % possible obs: 94.6 % / Redundancy: 3.6 % / Rmerge(I) obs: 0.064 / Rsym value: 0.056 / Net I/av σ(I): 20.86 / Net I/σ(I): 20.86
Reflection shellResolution: 2.17→2.21 Å / Redundancy: 3 % / Rmerge(I) obs: 0.186 / Mean I/σ(I) obs: 4.19 / % possible all: 59.7

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Processing

Software
NameVersionClassification
REFMAC5.8.0103refinement
PHASERphasing
HKL-3000data reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3VYN

3vyn


Resolution: 2.17→50 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.914 / SU B: 5.402 / SU ML: 0.138 / Cross valid method: THROUGHOUT / ESU R: 0.234 / ESU R Free: 0.199 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23386 2153 5 %RANDOM
Rwork0.18036 ---
obs0.18307 40491 95.45 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 27.029 Å2
Baniso -1Baniso -2Baniso -3
1-0.66 Å2-0 Å2-0.75 Å2
2--1.39 Å20 Å2
3----1.97 Å2
Refinement stepCycle: 1 / Resolution: 2.17→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5292 0 25 462 5779
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0195458
X-RAY DIFFRACTIONr_bond_other_d0.0020.025032
X-RAY DIFFRACTIONr_angle_refined_deg1.9291.9287460
X-RAY DIFFRACTIONr_angle_other_deg1.079311538
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.2745701
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.57924.093237
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.38315785
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.5481533
X-RAY DIFFRACTIONr_chiral_restr0.1280.2838
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0216322
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021263
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.9542.4972807
X-RAY DIFFRACTIONr_mcbond_other1.9542.4962806
X-RAY DIFFRACTIONr_mcangle_it2.8783.7343507
X-RAY DIFFRACTIONr_mcangle_other2.8783.7353508
X-RAY DIFFRACTIONr_scbond_it2.7482.7932651
X-RAY DIFFRACTIONr_scbond_other2.7432.7932651
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.0714.0593954
X-RAY DIFFRACTIONr_long_range_B_refined5.87620.8436298
X-RAY DIFFRACTIONr_long_range_B_other5.87620.8466299
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.174→2.23 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.286 147 -
Rwork0.216 2504 -
obs--80.87 %

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