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- PDB-5du7: Crystal structure of ldtMt2 at 1.79 Angstrom resolution -

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Basic information

Entry
Database: PDB / ID: 5du7
TitleCrystal structure of ldtMt2 at 1.79 Angstrom resolution
ComponentsL,D-transpeptidase 2
KeywordsTRANSFERASE / 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
L,D-transpeptidase 2 / L,D-transpeptidase 2
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.79 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
D: L,D-transpeptidase 2
C: L,D-transpeptidase 2


Theoretical massNumber of molelcules
Total (without water)158,1284
Polymers158,1284
Non-polymers00
Water32,9131827
1
A: 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
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
3
D: 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
4
C: 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
5
A: L,D-transpeptidase 2

D: L,D-transpeptidase 2


Theoretical massNumber of molelcules
Total (without water)79,0642
Polymers79,0642
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_556x,y,z+11
Buried area1770 Å2
ΔGint-16 kcal/mol
Surface area30850 Å2
MethodPISA
6
B: L,D-transpeptidase 2
C: L,D-transpeptidase 2


Theoretical massNumber of molelcules
Total (without water)79,0642
Polymers79,0642
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1750 Å2
ΔGint-15 kcal/mol
Surface area30890 Å2
MethodPISA
Unit cell
Length a, b, c (Å)61.644, 75.534, 94.143
Angle α, β, γ (deg.)89.040, 89.960, 92.760
Int Tables number1
Space group name H-MP1

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Components

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


Mass: 39532.004 Da / Num. of mol.: 4 / 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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1827 / 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: 2.91 Å3/Da / Density % sol: 57.73 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 20% PEG5000MME, 0.2mM 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: 0.979 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 17, 2015 / Details: MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.7→50 Å / Num. obs: 153919 / % possible obs: 97.3 % / Redundancy: 3.7 % / Rmerge(I) obs: 0.068 / Rpim(I) all: 0.041 / Rrim(I) all: 0.078 / Χ2: 0.768 / Net I/av σ(I): 14.832 / Net I/σ(I): 7.6 / Num. measured all: 676223
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allCC1/2Rpim(I) allΧ2% possible allRrim(I) all
1.7-1.733.50.888170.5770.5440.66995.7
1.73-1.763.70.76989470.6690.4660.69195.80.9
1.76-1.793.70.65488740.7110.3930.71396.10.763
1.79-1.833.80.52688940.8040.3150.73896.10.614
1.83-1.873.80.43889790.8480.2620.75596.40.511
1.87-1.913.80.33389440.8890.1990.81796.40.388
1.91-1.963.80.2889730.9020.1680.86196.70.327
1.96-2.023.80.22989540.9140.1370.85696.80.266
2.02-2.073.80.18590320.9270.1110.865970.216
2.07-2.143.80.15689570.940.0930.89897.20.182
2.14-2.223.80.13390760.9410.080.84497.30.155
2.22-2.313.80.11690680.950.0690.86297.50.135
2.31-2.413.80.10390220.9590.0620.86397.70.12
2.41-2.543.80.08991300.9620.0530.854980.104
2.54-2.73.80.07991130.9660.0470.84998.10.092
2.7-2.913.80.06991370.970.0410.80598.40.081
2.91-3.23.80.06191330.9720.0370.77898.60.072
3.2-3.663.70.05491920.9790.0320.695990.063
3.66-4.613.70.04691870.9850.0280.52799.20.054
4.61-503.70.04291280.9890.0250.38798.30.049

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
HKL-2000data collection
HKL-2000data scaling
PHASERphasing
REFMAC5.8.0103refinement
PDB_EXTRACT3.15data extraction
HKL-3000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3VYN

3vyn


Resolution: 1.79→50 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.933 / WRfactor Rfree: 0.2147 / WRfactor Rwork: 0.1714 / FOM work R set: 0.8531 / SU B: 2.685 / SU ML: 0.082 / SU R Cruickshank DPI: 0.1141 / SU Rfree: 0.1143 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.114 / ESU R Free: 0.114 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.21 7371 4.9 %RANDOM
Rwork0.1696 ---
obs0.1716 144115 94.72 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 82.66 Å2 / Biso mean: 17.48 Å2 / Biso min: 3.83 Å2
Baniso -1Baniso -2Baniso -3
1-0.17 Å20.04 Å20.1 Å2
2---0.25 Å2-0.07 Å2
3---0.08 Å2
Refinement stepCycle: final / Resolution: 1.79→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10558 0 0 1827 12385
Biso mean---30.73 -
Num. residues----1399
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.01910870
X-RAY DIFFRACTIONr_bond_other_d0.0020.029993
X-RAY DIFFRACTIONr_angle_refined_deg1.9911.92614877
X-RAY DIFFRACTIONr_angle_other_deg1.103322919
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.36451399
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.34924.093474
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.948151560
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.4121566
X-RAY DIFFRACTIONr_chiral_restr0.1540.21669
X-RAY DIFFRACTIONr_gen_planes_refined0.010.02112635
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022519
X-RAY DIFFRACTIONr_mcbond_it1.5661.4585611
X-RAY DIFFRACTIONr_mcbond_other1.5661.4585610
X-RAY DIFFRACTIONr_mcangle_it2.3982.1767005
LS refinement shellResolution: 1.79→1.836 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.269 414 -
Rwork0.243 7673 -
all-8087 -
obs--68.39 %

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