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- PDB-8pxy: Crystal structure of the transpeptidase LdtMt2 C354S mutant from ... -

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Basic information

Entry
Database: PDB / ID: 8pxy
TitleCrystal structure of the transpeptidase LdtMt2 C354S mutant from Mycobacterium tuberculosis in complex with natural substrate
Components
  • L,D-transpeptidase 2
  • Peptidoglycan tetrapeptide
KeywordsANTIMICROBIAL PROTEIN / LdtMt2 / Substrate complex / Mycobacterium tuberculosis / L / D-transpeptidase
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
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.
Similarity search - Domain/homology
L,D-transpeptidase 2
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.15 Å
Authorsde Munnik, M. / Schofield, C.J.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research Council (BBSRC) United Kingdom
CitationJournal: To Be Published
Title: Crystal structure of the transpeptidase LdtMt2 C354S mutant from Mycobacterium tuberculosis in complex with natural substrate
Authors: de Munnik, M. / Schofield, C.J.
History
DepositionJul 24, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 7, 2024Provider: repository / Type: Initial release

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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: Peptidoglycan tetrapeptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,2235
Polymers38,4532
Non-polymers7703
Water6,071337
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: mass spectrometry
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1210 Å2
ΔGint3 kcal/mol
Surface area16920 Å2
MethodPISA
Unit cell
Length a, b, c (Å)76.608, 94.623, 58.794
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11A-933-

HOH

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Components

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Protein / Protein/peptide / Sugars , 3 types, 3 molecules AB

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


Mass: 37993.082 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Gene: ldtB, MT2594, V735_02606 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: O53223, Transferases; Acyltransferases; Aminoacyltransferases
#2: Protein/peptide Peptidoglycan tetrapeptide


Mass: 459.496 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mycobacterium tuberculosis (bacteria)
#3: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-N-acetyl-alpha-muramic acid


Type: oligosaccharide / Mass: 496.463 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4MurNAc1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,2,1/[a2122h-1a_1-5_2*NCC/3=O_3*OC^RCO/4=O/3C][a2122h-1b_1-5_2*NCC/3=O]/1-2/a4-b1WURCSPDB2Glycan 1.1.0
[][a-D-GlcpNAc]{[(3+1)][<C3O1>]{}[(4+1)][b-D-GlcpNAc]{}}LINUCSPDB-CARE

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Non-polymers , 3 types, 339 molecules

#4: Chemical ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES


Mass: 238.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18N2O4S / Comment: pH buffer*YM
#5: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 337 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 2.8 Å3/Da / Density % sol: 56.14 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 0.1 M HEPES pH 7.0, 25% Jeffamine ED-2001 pH 7.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.97625 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: May 13, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97625 Å / Relative weight: 1
ReflectionResolution: 2.15→59.54 Å / Num. obs: 23935 / % possible obs: 100 % / Redundancy: 13.2 % / Biso Wilson estimate: 30.14 Å2 / CC1/2: 0.993 / Rmerge(I) obs: 0.138 / Rpim(I) all: 0.04 / Rrim(I) all: 0.144 / Net I/σ(I): 10.8
Reflection shellResolution: 2.15→2.19 Å / Redundancy: 13.5 % / Rmerge(I) obs: 0.987 / Mean I/σ(I) obs: 1.1 / Num. unique obs: 1136 / CC1/2: 0.844 / Rpim(I) all: 0.279 / Rrim(I) all: 1.027 / % possible all: 97

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Processing

Software
NameVersionClassification
PHENIX(1.18.2_3874: ???)refinement
DIALSdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.15→59.54 Å / SU ML: 0.3 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 24.51 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2463 1161 4.87 %
Rwork0.2006 --
obs0.2028 23830 99.57 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.15→59.54 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2619 0 81 337 3037
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0032807
X-RAY DIFFRACTIONf_angle_d0.5743857
X-RAY DIFFRACTIONf_dihedral_angle_d11.257960
X-RAY DIFFRACTIONf_chiral_restr0.048436
X-RAY DIFFRACTIONf_plane_restr0.003506
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.15-2.250.29121480.27132737X-RAY DIFFRACTION98
2.25-2.370.35351300.27072786X-RAY DIFFRACTION100
2.37-2.510.27381430.26042764X-RAY DIFFRACTION99
2.51-2.710.31661460.25282835X-RAY DIFFRACTION100
2.71-2.980.28421470.23152804X-RAY DIFFRACTION100
2.98-3.410.2471480.20392841X-RAY DIFFRACTION100
3.41-4.30.23751360.16632896X-RAY DIFFRACTION100
4.3-59.540.19021630.16623006X-RAY DIFFRACTION100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.6711-0.24262.2356.31790.52063.4060.0779-0.0210.0332-0.1614-0.0267-0.04160.3085-0.1702-0.05420.26890.01630.04450.2882-0.0070.306853.81777.088712.1721
22.7525-0.16880.53650.8555-0.05330.48320.0136-0.124-0.0103-0.1092-0.0123-0.07460.01710.06170.00520.31310.010.05230.29270.01080.236933.391617.579510.9384
31.4502-0.0705-0.29830.76220.14591.65230.0724-0.05580.0355-0.1579-0.08240.1332-0.2043-0.23330.01340.330.0343-0.07510.2855-0.00010.29512.599326.702513.7201
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 58 through 122 )
2X-RAY DIFFRACTION2chain 'A' and (resid 123 through 248 )
3X-RAY DIFFRACTION3chain 'A' and (resid 249 through 407 )

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