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- PDB-2mvo: Solution structure of the lantibiotic self-resistance lipoprotein... -

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Basic information

Entry
Database: PDB / ID: 2mvo
TitleSolution structure of the lantibiotic self-resistance lipoprotein MlbQ from Microbispora ATCC PTA-5024
ComponentsPutative lipoprotein
KeywordsLIPID BINDING PROTEIN / lipoprotein / lantibiotic resistance
Function / homologyProtein YebY / Protein of unknown function (DUF2511) / Putative lipoprotein
Function and homology information
Biological speciesMicrobispora sp. ATCC PTA-5024 (bacteria)
MethodSOLUTION NMR / simulated annealing, NOESY back-calculation
Model detailsminimized average structure, model1
Model type detailsminimized average
AuthorsPozzi, R. / Schwartz, P. / Linke, D. / Kulik, A. / Nega, M. / Wohlleben, W. / Stegmann, E. / Coles, M.
CitationJournal: Environ Microbiol / Year: 2016
Title: Distinct mechanisms contribute to immunity in the lantibiotic NAI-107 producer strain Microbispora ATCC PTA-5024.
Authors: Pozzi, R. / Coles, M. / Linke, D. / Kulik, A. / Nega, M. / Wohlleben, W. / Stegmann, E.
History
DepositionOct 9, 2014Deposition site: BMRB / Processing site: RCSB
Revision 1.0Jul 15, 2015Provider: repository / Type: Initial release
Revision 1.1Mar 23, 2016Group: Database references
Revision 1.2Jun 14, 2023Group: Data collection / Database references / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_software / pdbx_nmr_spectrometer / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model / _struct_ref_seq_dif.details
Revision 1.3Nov 6, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Putative lipoprotein


Theoretical massNumber of molelcules
Total (without water)15,4561
Polymers15,4561
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100structures with the least restraint violations
RepresentativeModel #1minimized average structure

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Components

#1: Protein Putative lipoprotein


Mass: 15456.088 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Microbispora sp. ATCC PTA-5024 (bacteria)
Strain: ATCC PTA-5024 / Gene: mlbQ / Production host: Escherichia coli (E. coli) / References: UniProt: W2EQT0
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1123D HNCO
1223D C(CO)NH
1323D (H)CCH-TOCSY
1423D CCH NOESY
1523D CNH NOESY
1613D 1H-15N NOESY
1723D 1H-13C NOESY
1813D HNHA
1913D HNHB
11023D 3JHBHA(CO)NH
11113D NNH NOESY
11223D HN(CA)NNH
11323D HNCA

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Sample preparation

Details
Solution-IDContentsSolvent system
10.5 mM [U-100% 15N] MlbQ, 20 mM TRIS, 250 mM sodium chloride, 90% H2O/10% D2O90% H2O/10% D2O
20.5 mM [U-100% 13C; U-100% 15N] MlbQ, 20 mM TRIS, 250 mM sodium chloride, 90% H2O/10% D2O90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.5 mMMlbQ-1[U-100% 15N]1
20 mMTRIS-21
250 mMsodium chloride-31
0.5 mMMlbQ-4[U-100% 13C; U-100% 15N]2
20 mMTRIS-52
250 mMsodium chloride-62
Sample conditionsIonic strength: 0.24 / pH: 8 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AvanceBrukerAVANCE6001
Bruker AvanceBrukerAVANCE8002

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Processing

NMR software
NameVersionDeveloperClassification
TopSpinBruker Biospincollection
TopSpinBruker Biospinprocessing
SparkyGoddardchemical shift assignment
SparkyGoddarddata analysis
X-PLOR NIH2.9.4Schwieters, Kuszewski, Tjandra and Clorestructure solution
X-PLOR NIH2.9.4Schwieters, Kuszewski, Tjandra and Clorerefinement
NMR-SPIRIT1.1In houserefinement
RefinementMethod: simulated annealing, NOESY back-calculation / Software ordinal: 1
NMR constraintsProtein chi angle constraints total count: 65 / Protein other angle constraints total count: 47 / Protein phi angle constraints total count: 137 / Protein psi angle constraints total count: 191
NMR representativeSelection criteria: minimized average structure
NMR ensembleConformer selection criteria: structures with the least restraint violations
Conformers calculated total number: 100 / Conformers submitted total number: 20 / Maximum lower distance constraint violation: 0.01 Å / Maximum torsion angle constraint violation: 0.8 ° / Maximum upper distance constraint violation: 0.13 Å
NMR ensemble rmsDistance rms dev: 0.017 Å / Distance rms dev error: 0.001 Å

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