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- PDB-3u1q: Crystal Structure of M. tuberculosis LD-transpeptidase type 2 wit... -

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Basic information

Entry
Database: PDB / ID: 3u1q
TitleCrystal Structure of M. tuberculosis LD-transpeptidase type 2 with 2-Mercaptoethanol
ComponentsMycobacteria Tuberculosis LD-transpeptidase type 2
KeywordsPEPTIDOGLYCAN BINDING PROTEIN / protein-peptidoglycan complex
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 / 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
BETA-MERCAPTOETHANOL / DI(HYDROXYETHYL)ETHER / L,D-transpeptidase 2
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsErdemli, S. / Bianchet, M.A. / Gupta, R. / Lamichhane, G. / Amzel, L.M.
CitationJournal: to be published
Title: The Structure of Mycobacterium tuberculosis L,D-transpeptidase 2 provides insights into targeting the cell wall of persisters
Authors: Erdemli, S.B. / Gupta, R. / Lamichhane, G. / Bishai, W. / Amzel, L.M. / Bianchet, M.A.
History
DepositionSep 30, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 5, 2012Provider: repository / Type: Initial release
Revision 1.1Apr 4, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.type
Revision 1.2Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_special_symmetry / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Mycobacteria Tuberculosis LD-transpeptidase type 2
B: Mycobacteria Tuberculosis LD-transpeptidase type 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,20412
Polymers62,2552
Non-polymers94910
Water4,017223
1
A: Mycobacteria Tuberculosis LD-transpeptidase type 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,4965
Polymers31,1281
Non-polymers3694
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Mycobacteria Tuberculosis LD-transpeptidase type 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,7087
Polymers31,1281
Non-polymers5816
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4220 Å2
ΔGint-1 kcal/mol
Surface area21640 Å2
MethodPISA
Unit cell
Length a, b, c (Å)117.689, 121.013, 122.799
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number24
Space group name H-MI212121
Components on special symmetry positions
IDModelComponents
11B-701-

HOH

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Components

#1: Protein Mycobacteria Tuberculosis LD-transpeptidase type 2


Mass: 31127.539 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Gene: lppS, MT2594, Rv2518c / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: O53223
#2: Chemical
ChemComp-BME / BETA-MERCAPTOETHANOL


Mass: 78.133 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6OS
#3: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C4H10O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 223 / 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: 3.51 Å3/Da / Density % sol: 64.97 %
Crystal growTemperature: 298 K / Method: hanging drop / pH: 7.5
Details: 0.1 M Hepes (pH 7.5), 1 M succinic Acid, 1% (w/v) PEG MME 2000, hanging drop, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: OTHER / Wavelength: 1.5418 Å
DetectorType: RIGAKU SATURN 944+ / Detector: CCD / Date: Jan 1, 2009
RadiationMonochromator: VARIMAX / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.4→15.52 Å / Num. obs: 34413
Reflection shellNum. unique all: 34413

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Processing

Software
NameVersionClassificationNB
REFMAC5.5.0072refinement
PDB_EXTRACT3.1data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.4→15.52 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.921 / Occupancy max: 1 / SU B: 5.481 / SU ML: 0.133 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.217 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS; U VALUES: REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2442 1743 5.1 %RANDOM
Rwork0.1854 ---
obs0.1884 34413 99.79 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 87.12 Å2 / Biso mean: 36.5363 Å2 / Biso min: 15.61 Å2
Baniso -1Baniso -2Baniso -3
1-3.64 Å20 Å20 Å2
2---1.24 Å20 Å2
3----2.39 Å2
Refinement stepCycle: LAST / Resolution: 2.4→15.52 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3998 0 58 223 4279
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0230.0214204
X-RAY DIFFRACTIONr_angle_refined_deg1.9051.9225730
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5025529
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.89224.301193
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.91815607
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.5271522
X-RAY DIFFRACTIONr_chiral_restr0.1380.2615
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0213276
X-RAY DIFFRACTIONr_mcbond_it1.0951.52596
X-RAY DIFFRACTIONr_mcangle_it2.04724216
X-RAY DIFFRACTIONr_scbond_it3.56431608
X-RAY DIFFRACTIONr_scangle_it5.5434.51511
LS refinement shellResolution: 2.4→2.461 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.312 131 -
Rwork0.226 2355 -
all-2486 -
obs--99.92 %

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