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- PDB-8byk: The structure of MadC from Clostridium maddingley reveals new ins... -

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Basic information

Entry
Database: PDB / ID: 8byk
TitleThe structure of MadC from Clostridium maddingley reveals new insights into class I lanthipeptide cyclases
ComponentsLanthionine synthetase C-like protein
KeywordsBIOSYNTHETIC PROTEIN / cyclase / lantibiotic / biosynthetic
Function / homology
Function and homology information


peptide modification / metal ion binding / plasma membrane
Similarity search - Function
Subtilin biosynthesis protein SpaC / Type I lantibiotic biosynthesis cyclase / Lanthionine synthetase C-like protein / Lanthionine synthetase C-like protein / Lanthionine synthetase C-like / Glycosyltransferase - #20 / Glycosyltransferase / Alpha/alpha barrel / Mainly Alpha
Similarity search - Domain/homology
ACETATE ION / Lanthionine synthetase C-like protein
Similarity search - Component
Biological speciesClostridium (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsKnospe, C.V. / Kamel, M. / Spitz, O. / Hoeppner, A. / Galle, S. / Reiners, J. / Kedrov, A. / Smits, S.H. / Schmitt, L.
Funding support Germany, 2items
OrganizationGrant numberCountry
German Research Foundation (DFG)Schm1279/13-1 Germany
German Research Foundation (DFG)417919780 Germany
CitationJournal: Front Microbiol / Year: 2022
Title: The structure of MadC from Clostridium maddingley reveals new insights into class I lanthipeptide cyclases.
Authors: Knospe, C.V. / Kamel, M. / Spitz, O. / Hoeppner, A. / Galle, S. / Reiners, J. / Kedrov, A. / Smits, S.H.J. / Schmitt, L.
History
DepositionDec 13, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 22, 2023Provider: repository / Type: Initial release
Revision 1.1Jun 19, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Lanthionine synthetase C-like protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,3819
Polymers50,8201
Non-polymers5608
Water5,296294
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: SAXS
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1510 Å2
ΔGint-65 kcal/mol
Surface area17170 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.140, 66.119, 117.258
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

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Protein , 1 types, 1 molecules A

#1: Protein Lanthionine synthetase C-like protein


Mass: 50820.453 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Clostridium (bacteria) / Gene: A370_05564 / Production host: Escherichia coli (E. coli) / References: UniProt: K6THC9

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Non-polymers , 6 types, 302 molecules

#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#4: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#5: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#6: Chemical ChemComp-CL / CHLORIDE ION


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


Mass: 18.015 Da / Num. of mol.: 294 / 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: 2.07 Å3/Da / Density % sol: 40.49 %
Crystal growTemperature: 298 K / Method: vapor diffusion / Details: lithium chloride and MPD

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X13 / Wavelength: 0.9763 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Aug 2, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 1.7→41.89 Å / Num. obs: 47068 / % possible obs: 99.97 % / Redundancy: 13 % / CC1/2: 0.999 / Net I/σ(I): 29.63
Reflection shellResolution: 1.7→1.761 Å / Num. unique obs: 4591 / CC1/2: 0.995

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Processing

Software
NameVersionClassification
REFMAC5.8.0131refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.7→41.89 Å / Cross valid method: FREE R-VALUE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.22 --
Rwork0.19 --
obs-47059 99 %
Displacement parametersBiso mean: 24.47 Å2
Refinement stepCycle: LAST / Resolution: 1.7→41.89 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3418 0 32 294 3744
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.02743676
X-RAY DIFFRACTIONf_angle_d2.20945004
X-RAY DIFFRACTIONf_chiral_restr0.1613542
X-RAY DIFFRACTIONf_plane_restr0.0142652
X-RAY DIFFRACTIONf_dihedral_angle_d21.23831354

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