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- PDB-6st5: crystal structure of LicM2 -

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Basic information

Entry
Database: PDB / ID: 6st5
Titlecrystal structure of LicM2
ComponentsLicM2
KeywordsANTIMICROBIAL PROTEIN / crystal / ATP
Function / homology
Function and homology information


peptide modification / carbohydrate metabolic process
Similarity search - Function
Type 2 lantibiotic biosynthesis protein LanM / Lantibiotic biosynthesis protein, dehydration domain / Domain of unknown function (DUF4135) / Lanthionine synthetase C-like protein / Lanthionine synthetase C-like protein / Lanthionine synthetase C-like / Six-hairpin glycosidase-like superfamily
Similarity search - Domain/homology
PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / LicM2
Similarity search - Component
Biological speciesBacillus licheniformis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.82 Å
AuthorsGonsior, M. / Mainz, A. / Hugelland, M. / Kuthning, A. / Tietzmann, M. / Dobbek, H. / Martins, B.M. / Sussmuth, R.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research Foundation (DFG)EXC 2008 1 390540038 Germany
CitationJournal: To Be Published
Title: crystal structure of LicM2
Authors: Gonsior, M. / Martins, B.M.
History
DepositionSep 10, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 10, 2022Provider: repository / Type: Initial release
Revision 1.1Nov 13, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature
Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: LicM2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)112,56312
Polymers111,2301
Non-polymers1,33311
Water181
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)78.365, 128.408, 141.220
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 1 molecules A

#1: Protein LicM2


Mass: 111230.234 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus licheniformis (bacteria) / Gene: licM2 / Production host: Escherichia coli (E. coli) / References: UniProt: E9MWH4

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Non-polymers , 5 types, 12 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-ANP / PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER


Mass: 506.196 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H17N6O12P3 / Feature type: SUBJECT OF INVESTIGATION / Comment: AMP-PNP, energy-carrying molecule analogue*YM
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
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: 3 Å3/Da / Density % sol: 56 % / Description: long pencil-shaped
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 0.1 M MgCl2, 0.1 M MOPS, 12% PEG 8000 / Temp details: incubator

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.979568 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: May 24, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979568 Å / Relative weight: 1
ReflectionResolution: 2.817→47.503 Å / Num. obs: 35085 / % possible obs: 99.7 % / Redundancy: 13 % / Rmerge(I) obs: 0.19 / Net I/σ(I): 8.96
Reflection shellResolution: 2.82→2.92 Å / Rmerge(I) obs: 0.299 / Mean I/σ(I) obs: 0.55 / Num. unique obs: 3435

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Processing

Software
NameVersionClassification
PHENIX1.11.1-2575_1168refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
XDSdata scaling
SHELXDEphasing
RefinementMethod to determine structure: SAD / Resolution: 2.82→47.5 Å / SU ML: 0.55 / Cross valid method: THROUGHOUT / σ(F): 1.31 / Phase error: 32.71
RfactorNum. reflection% reflection
Rfree0.272 2094 3.16 %
Rwork0.224 64265 -
obs0.225 66359 99.7 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 239.41 Å2 / Biso mean: 90 Å2 / Biso min: 30 Å2
Refinement stepCycle: final / Resolution: 2.82→47.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7257 0 202 1 7460
Biso mean--113.98 72.67 -
Num. residues----913
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.82-2.88230.45911410.3861423898
2.8823-2.95440.36931410.3604423999
2.9544-3.03430.37851400.33884294100
3.0343-3.12350.37381400.35594329100
3.1235-3.22430.42381400.31384287100
3.2243-3.33960.34831370.28524277100
3.3396-3.47320.32371420.26324306100
3.4732-3.63120.33021390.2434279100
3.6312-3.82260.26421410.21664325100
3.8226-4.0620.2471360.1851426399
4.062-4.37540.2191380.17284301100
4.3754-4.81540.20051400.15914284100
4.8154-5.51120.20561370.18554298100
5.5112-6.94010.26461370.23424272100
6.9401-47.50.26261450.2174427399

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