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- PDB-2mfv: Structure of lasso peptide xanthomonin ii -

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Basic information

Entry
Database: PDB / ID: 2mfv
TitleStructure of lasso peptide xanthomonin ii
ComponentsXanthomonin II
KeywordsUNKNOWN FUNCTION / LASSO PEPTIDE / SEVEN-RESIDUE LASSO RING
Function / homologyUncharacterized protein
Function and homology information
Biological speciesXanthomonas gardneri (bacteria)
MethodSOLUTION NMR / simulated annealing
Model detailslowest energy, model 1
AuthorsHegemann, J.D. / Zimmermann, M. / Harms, K. / Xie, X. / Marahiel, M.A.
CitationJournal: To be Published
Title: Xanthomonin I-III are Lasso Peptides Featuring Macrolactam Rings Consisting of Only Seven Amino Acids
Authors: Hegemann, J.D. / Zimmermann, M. / Zhu, S. / Harms, H.S. / Xie, X. / Marahiel, M.A.
History
DepositionOct 23, 2013Deposition site: BMRB / Processing site: RCSB
Revision 1.0Oct 29, 2014Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Xanthomonin II


Theoretical massNumber of molelcules
Total (without water)1,2891
Polymers1,2891
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)15 / 50target function
RepresentativeModel #1lowest energy

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Components

#1: Protein/peptide Xanthomonin II


Mass: 1289.413 Da / Num. of mol.: 1 / Fragment: UNP residues 29-42
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Xanthomonas gardneri (bacteria) / Strain: ATCC 19865 / Gene: XGAA2, XGA_4059 / Plasmid: PET41A / Production host: Xanthomonas gardneri (bacteria) / Strain (production host): DSM19127 / References: UniProt: F0CAT1

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D DQF-COSY
1212D 1H-1H TOCSY
1312D 1H-1H NOESY

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Sample preparation

DetailsContents: 8.8 mM XANTHOMONIN II, DMSO / Solvent system: DMSO
SampleConc.: 8.8 mM / Component: XANTHOMONIN II-1
Sample conditionsPressure: ambient / Temperature: 305 K

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NMR measurement

NMR spectrometerType: Bruker Avance / Manufacturer: Bruker / Model: Avance / Field strength: 600 MHz

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Processing

NMR software
NameVersionDeveloperClassification
CYANA2.1Guntert, Mumenthaler and Wuthrichstructure solution
CYANArefinement
RefinementMethod: simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 50 / Conformers submitted total number: 15

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