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- PDB-8yoa: Crystal structure of endolytic transglycosylase MltG -

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Basic information

Entry
Database: PDB / ID: 8yoa
TitleCrystal structure of endolytic transglycosylase MltG
ComponentsEndolytic murein transglycosylase
KeywordsLYASE / MltG / Lytic transglycosylase / Peptidoglycan / Membrane binding protein / MEMBRANE PROTEIN
Function / homologypeptidoglycan lytic transglycosylase / Endolytic murein transglycosylase / YceG-like family / lytic endotransglycosylase activity / peptidoglycan biosynthetic process / cell wall organization / plasma membrane / Endolytic murein transglycosylase
Function and homology information
Biological speciesMycobacteroides abscessus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsLee, G.H. / Park, H.H.
Funding support Korea, Republic Of, 1items
OrganizationGrant numberCountry
National Research Foundation (NRF, Korea) Korea, Republic Of
CitationJournal: Iucrj / Year: 2024
Title: Structure of MltG from Mycobacterium abscessus reveals structural plasticity between composed domains.
Authors: Lee, G.H. / Kim, S. / Kim, D.Y. / Han, J.H. / Lee, S.Y. / Lee, J.H. / Lee, C.S. / Park, H.H.
History
DepositionMar 13, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 13, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Endolytic murein transglycosylase


Theoretical massNumber of molelcules
Total (without water)37,3841
Polymers37,3841
Non-polymers00
Water2,558142
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: light scattering
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)43.220, 63.240, 123.560
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

#1: Protein Endolytic murein transglycosylase / Peptidoglycan polymerization terminase


Mass: 37383.527 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacteroides abscessus (bacteria) / Gene: yceG, mltG, ERS075579_00491 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: A0A0U1AN13, Lyases; Carbon-oxygen lyases; Acting on polysaccharides
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 142 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.26 Å3/Da / Density % sol: 45.54 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop
Details: 0.9M Sodium Citrate, 0.1M Tris pH 7.4, 0.2M NaCl, 40% (V/V) Acetone

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Data collection

DiffractionMean temperature: 125 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 5C (4A) / Wavelength: 1 Å
DetectorType: DECTRIS EIGER2 X 9M / Detector: PIXEL / Date: Jul 7, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.2→29.82 Å / Num. obs: 17774 / % possible obs: 99.37 % / Redundancy: 12.5 % / Biso Wilson estimate: 30.24 Å2 / Rmerge(I) obs: 0.2455 / Net I/σ(I): 16.51
Reflection shellResolution: 2.2→2.279 Å / Num. unique obs: 1735 / CC1/2: 0.919

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XDSdata reduction
XDSdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.2→29.82 Å / SU ML: 0.2214 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 20.9681
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2193 889 5 %
Rwork0.1815 16881 -
obs0.1834 17770 99.44 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 33.3 Å2
Refinement stepCycle: LAST / Resolution: 2.2→29.82 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2629 0 0 142 2771
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00822674
X-RAY DIFFRACTIONf_angle_d0.86723635
X-RAY DIFFRACTIONf_chiral_restr0.0509414
X-RAY DIFFRACTIONf_plane_restr0.0097485
X-RAY DIFFRACTIONf_dihedral_angle_d5.6442374
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2-2.340.25751450.20552747X-RAY DIFFRACTION98.91
2.34-2.520.29671460.20732779X-RAY DIFFRACTION99.66
2.52-2.770.26681450.21282756X-RAY DIFFRACTION99.49
2.77-3.170.24971480.19562817X-RAY DIFFRACTION99.76
3.17-40.19351490.16952833X-RAY DIFFRACTION99.97
4-29.820.17861560.16072949X-RAY DIFFRACTION98.92

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