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

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Basic information

Entry
Database: PDB / ID: 5dzp
TitleCrystal structure of Mycobacterium tuberculosis L,D-transpeptidase 2 with carbapenem drug T206 in conformation B
ComponentsL,D-transpeptidase 2
KeywordsTRANSFERASE / Peptidoglycan synthesis enzyme / cell wall enzyme
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 / extracellular region / 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 / L,D-transpeptidase catalytic domain-like / Prokaryotic membrane lipoprotein lipid attachment site profile. ...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 / L,D-transpeptidase catalytic domain-like / Prokaryotic membrane lipoprotein lipid attachment site profile. / Immunoglobulin-like / Beta Barrel / Sandwich / Mainly Beta
Similarity search - Domain/homology
Chem-6B7 / L,D-transpeptidase 2
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.19 Å
AuthorsKumar, P. / Ginell, S.L. / Lamichhane, G.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/Office of the Director1DP2OD008459-01 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)1R21AI111739-01 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 25, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 5, 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 1.5Dec 11, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.6Sep 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

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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)79,4093
Polymers79,0642
Non-polymers3451
Water11,440635
1
A: L,D-transpeptidase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,8772
Polymers39,5321
Non-polymers3451
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: L,D-transpeptidase 2


Theoretical massNumber of molelcules
Total (without water)39,5321
Polymers39,5321
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)61.518, 93.874, 75.318
Angle α, β, γ (deg.)90.00, 92.78, 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 (strain ATCC 25618 / H37Rv) (bacteria)
Strain: ATCC 25618 / H37Rv / Gene: ldtB, lppS, Rv2518c, RVBD_2518c, P425_02624 / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: I6Y9J2, Transferases; Acyltransferases; Aminoacyltransferases
#2: Chemical ChemComp-6B7 / (2~{R},3~{R},4~{R})-4-methyl-3-(2-oxidanylidene-2-propoxy-ethyl)sulfanyl-5-[(2~{S},3~{R})-3-oxidanyl-1-oxidanylidene-butan-2-yl]-3,4-dihydro-2~{H}-pyrrole-2-carboxylic acid


Mass: 345.411 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H23NO6S
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 635 / Source method: isolated from a natural source / Formula: H2O

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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: 2.75 Å3/Da / Density % sol: 55.23 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / Details: PEG5000MME, Ammonium sulfate / PH range: pH 8.0

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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 315 / Detector: CCD / Date: Mar 16, 2015 / Details: mirrors
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 2.19→75.23 Å / Num. obs: 43836 / % possible obs: 99.6 % / Redundancy: 6.9 % / Rmerge(I) obs: 0.12 / Rpim(I) all: 0.049 / Rrim(I) all: 0.13 / Χ2: 0.932 / Net I/av σ(I): 15.839 / Net I/σ(I): 6.3 / Num. measured all: 304379
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.19-2.246.20.52121440.90.2250.5690.68899
2.24-2.286.30.49921780.9140.2130.5440.69698.9
2.28-2.326.60.4821610.9250.20.5210.70999.4
2.32-2.376.70.4522000.9240.1860.4880.72199.2
2.37-2.426.90.42721400.9360.1760.4630.7399.4
2.42-2.486.90.36821950.9490.1510.3980.75699.4
2.48-2.546.90.32921700.9660.1340.3560.74599.6
2.54-2.6170.30721700.9650.1250.3320.79299.6
2.61-2.6970.27522220.9710.1120.2970.81299.6
2.69-2.777.10.23521620.9770.0950.2540.84899.8
2.77-2.877.10.20521940.9810.0830.2220.92399.7
2.87-2.997.10.17222040.9840.0690.1860.99799.9
2.99-3.127.10.14821920.9890.060.161.11199.9
3.12-3.297.10.12722000.9890.0510.1371.20699.9
3.29-3.497.20.11121800.9920.0450.121.318100
3.49-3.767.10.09422100.9930.0380.1021.314100
3.76-4.1470.08222240.9940.0330.0891.242100
4.14-4.747.10.06722290.9960.0270.0721.131100
4.74-5.977.40.0622020.9960.0240.0650.898100
5.97-507.10.05722590.9920.0240.0620.86599.6

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Processing

Software
NameVersionClassification
REFMAC5.8.0103refinement
HKL-3000data scaling
PDB_EXTRACT3.15data extraction
HKL-3000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3VYN

3vyn


Resolution: 2.19→75.23 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.916 / SU B: 6.182 / SU ML: 0.155 / Cross valid method: THROUGHOUT / ESU R: 0.2 / ESU R Free: 0.21 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.24936 2219 5.1 %RANDOM
Rwork0.17959 ---
obs0.18305 41597 99.1 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 29.749 Å2
Baniso -1Baniso -2Baniso -3
1-0.73 Å2-0 Å2-0.23 Å2
2--1.81 Å2-0 Å2
3----2.51 Å2
Refinement stepCycle: LAST / Resolution: 2.19→75.23 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5271 0 23 635 5929
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0195427
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.9151.9277429
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.3285698
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.87124.274234
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.32415772
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.2061530
X-RAY DIFFRACTIONr_chiral_restr0.1250.2838
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0214198
X-RAY DIFFRACTIONr_gen_planes_other
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_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.188→2.244 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.282 164 -
Rwork0.226 2816 -
obs--92.03 %

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