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- PDB-9zn4: Solution NMR structure of the MppE leader peptide, a Nif11 RiPP f... -

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Basic information

Entry
Database: PDB / ID: 9zn4
TitleSolution NMR structure of the MppE leader peptide, a Nif11 RiPP from Moorena producens
ComponentsNif11 domain-containing protein
KeywordsBIOSYNTHETIC PROTEIN / RiPP leader peptide / a nif11-related precursor family
Function / homologyNif11 domain / Nif11-like leader peptide / Nif11 domain / Nif11 domain-containing protein
Function and homology information
Biological speciesMoorena producens (bacteria)
MethodSOLUTION NMR / matrix relaxation
AuthorsVidya, F.N.U. / McShan, A.C. / Agarwal, A.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)1R35GM142882 United States
CitationJournal: To Be Published
Title: Solution NMR structure of the MppE leader peptide, a Nif11 RiPP from Moorena producens
Authors: Vidya, F.N.U. / McShan, A.C. / Agarwal, A.
History
DepositionDec 12, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 24, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Nif11 domain-containing protein


Theoretical massNumber of molelcules
Total (without water)8,7311
Polymers8,7311
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: NMR Distance Restraints, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)10 / 30000structures with the lowest energy
RepresentativeModel #1closest to the average

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Components

#1: Protein Nif11 domain-containing protein


Mass: 8731.419 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Moorena producens (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: A0A1D8TKK6
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
111isotropic12D 1H-15N HSQC
121isotropic13D CBCA(CO)NH
131isotropic13D HN(CA)CB
141isotropic13D 1H-15N NOESY
151isotropic13D HNCO

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Sample preparation

DetailsType: solution / Contents: 0.3 mM [U-13C; U-15N] MppE, 90% H2O/10% D2O / Label: 15N 13C / Solvent system: 90% H2O/10% D2O
SampleConc.: 0.3 mM / Component: MppE / Isotopic labeling: [U-13C; U-15N]
Sample conditionsIonic strength: 100 mM / Label: CONDITIONS_1 / pH: 6.5 / 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
CS-ROSETTAShen, Vernon, Baker and Baxrefinement
CS-ROSETTAShen, Vernon, Baker and Baxstructure calculation
NMRFAM-SPARKYLeechemical shift assignment
NMRFAM-SPARKYLeepeak picking
RefinementMethod: matrix relaxation / Software ordinal: 1
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 30000 / Conformers submitted total number: 10

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