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- PDB-5wox: NMR solution structure of KanY protein (ms6282) using two 4D-spectra -

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Basic information

Entry
Database: PDB / ID: 5wox
TitleNMR solution structure of KanY protein (ms6282) using two 4D-spectra
ComponentsUncharacterized protein
KeywordsUNKNOWN FUNCTION / predicted polyketide cyclase/dehydratase
Function / homologyUncharacterised conserved protein UCP017371 / Polyketide cyclase/dehydrase / Polyketide cyclase / dehydrase and lipid transport / START-like domain superfamily / KanY protein / KanY protein
Function and homology information
Biological speciesMycobacterium smegmatis (bacteria)
MethodSOLUTION NMR / na
AuthorsEvangelidis, T. / Nerli, S. / Sgourakis, N.G. / Tripsianes, K.
CitationJournal: Nat Commun / Year: 2018
Title: Automated NMR resonance assignments and structure determination using a minimal set of 4D spectra.
Authors: Evangelidis, T. / Nerli, S. / Novacek, J. / Brereton, A.E. / Karplus, P.A. / Dotas, R.R. / Venditti, V. / Sgourakis, N.G. / Tripsianes, K.
History
DepositionAug 3, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 7, 2018Provider: repository / Type: Initial release
Revision 1.1May 1, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_nmr_software / pdbx_nmr_spectrometer
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Uncharacterized protein


Theoretical massNumber of molelcules
Total (without water)15,2851
Polymers15,2851
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area0 Å2
ΔGint0 kcal/mol
Surface area7260 Å2
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)10 / 100structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Uncharacterized protein


Mass: 15285.261 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155) (bacteria)
Strain: ATCC 700084 / mc(2)155 / Gene: MSMEI_6117 / Production host: Escherichia coli (E. coli) / References: UniProt: I7FUI2, UniProt: A0R5R3*PLUS

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic14D HC(CC TOCSY(CO))NH
121isotropic14D 13C,15N edited HMQC-NOESY-HSQC
131isotropic14D 13C,13C edited HMQC-NOESY-HSQC

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Sample preparation

DetailsType: solution
Contents: 1.2 mM [U-13C; U-15N] KanY protein ms6282, 93% H2O/7% D2O
Label: 13C_15N_sample / Solvent system: 93% H2O/7% D2O
SampleConc.: 1.2 mM / Component: KanY protein ms6282 / Isotopic labeling: [U-13C; U-15N]
Sample conditionsIonic strength: 150 mM / Label: condition_1 / pH: 6.5 / Pressure: 1 atm / Temperature: 298 K

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NMR measurement

NMR spectrometerType: Bruker AVANCE III / Manufacturer: Bruker / Model: AVANCE III / Field strength: 850 MHz

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Processing

NMR software
NameDeveloperClassification
4D-CHAINSEvangelidis and Tripsianeschemical shift assignment
CS-ROSETTAShen, Vernon, Baker and Baxrefinement
CS-ROSETTAShen, Vernon, Baker and Baxdata analysis
SparkyGoddardpeak picking
CS-ROSETTAShen, Vernon, Baker and Baxstructure calculation
RefinementMethod: na / Software ordinal: 2
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 10

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