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- PDB-9cjx: Solution NMR structure of the RiPP proteusin DprE2 from Desulfoto... -

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Basic information

Entry
Database: PDB / ID: 9cjx
TitleSolution NMR structure of the RiPP proteusin DprE2 from Desulfotomaculum sp.
ComponentsNHLP leader peptide family natural product
KeywordsBIOSYNTHETIC PROTEIN / proteusin / RiPP / leader peptide
Function / homologyNHLP leader peptide domain / Nitrile hydratase alpha /Thiocyanate hydrolase gamma superfamily / catalytic activity / transition metal ion binding / NHLP leader peptide family natural product
Function and homology information
Biological speciesDesulfotomaculum sp. (bacteria)
MethodSOLUTION NMR / matrix relaxation
AuthorsMcShan, A.C. / Agarwal, V. / Vidya, F.N.U.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35GM142882 United States
CitationJournal: To Be Published
Title: Solution NMR structure of the RiPP proteusin DprE2
Authors: McShan, A.C. / Agarwal, V. / Vidya, F.N.U.
History
DepositionJul 8, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 4, 2024Provider: repository / Type: Initial release
Revision 1.1Dec 11, 2024Group: Data collection / Refinement description / Category: pdbx_nmr_refine / pdbx_nmr_software
Item: _pdbx_nmr_refine.software_ordinal / _pdbx_nmr_software.classification

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Structure visualization

Structure viewerMolecule:
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Assembly

Deposited unit
A: NHLP leader peptide family natural product


Theoretical massNumber of molelcules
Total (without water)11,4481
Polymers11,4481
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: NMR Distance Restraints, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)10 / 10000structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein NHLP leader peptide family natural product / DprE2


Mass: 11447.863 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Desulfotomaculum sp. (bacteria) / Gene: DEF36_00885 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A358QQR8
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic13D HNCA
121isotropic13D HN(CA)CB
131isotropic13D HNCO
141isotropic13D CBCA(CO)NH
151isotropic13D 1H-15N NOESY

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Sample preparation

DetailsType: solution / Contents: 192 uM [U-13C; U-15N] DprE2, 90% H2O/10% D2O / Details: 15N,13C labeled DprE2 / Label: DprE2_NMR / Solvent system: 90% H2O/10% D2O
SampleConc.: 192 uM / Component: DprE2 / Isotopic labeling: [U-13C; U-15N]
Sample conditionsIonic strength: 100 mM / Label: conditions_1 / pH: 7 / Pressure: 1 atm / Temperature: 298 K

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NMR measurement

NMR spectrometerType: Bruker AVANCE III HD / Manufacturer: Bruker / Model: AVANCE III HD / Field strength: 800 MHz

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Processing

NMR software
NameDeveloperClassification
SparkyGoddardchemical shift assignment
CS-ROSETTAShen, Vernon, Baker and Baxrefinement
CS-ROSETTAShen, Vernon, Baker and Baxstructure calculation
RefinementMethod: matrix relaxation / Software ordinal: 2
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 10000 / Conformers submitted total number: 10

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