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- PDB-2mvj: Structure of Stage V sporulation protein M (SpoVM) P9A mutant -

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Basic information

Entry
Database: PDB / ID: 2mvj
TitleStructure of Stage V sporulation protein M (SpoVM) P9A mutant
ComponentsStage V sporulation protein M
KeywordsPROTEIN BINDING / membrane protein / membrane curvature
Function / homologySporulation stage V, protein M / Stage V sporulation protein family / sporulation resulting in formation of a cellular spore / membrane / Stage V sporulation protein M
Function and homology information
Biological speciesBacillus subtilis (bacteria)
MethodSOLUTION NMR / simulated annealing
AuthorsTian, F. / Gill Jr., R.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2015
Title: Structural basis for the geometry-driven localization of a small protein.
Authors: Gill, R.L. / Castaing, J.P. / Hsin, J. / Tan, I.S. / Wang, X. / Huang, K.C. / Tian, F. / Ramamurthi, K.S.
History
DepositionOct 7, 2014Deposition site: BMRB / Processing site: RCSB
Revision 1.0Apr 1, 2015Provider: repository / Type: Initial release
Revision 1.1Apr 15, 2015Group: Database references
Revision 1.2Apr 29, 2015Group: Database references
Revision 1.3Jun 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Stage V sporulation protein M


Theoretical massNumber of molelcules
Total (without water)2,9981
Polymers2,9981
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)10 / 50structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein/peptide Stage V sporulation protein M


Mass: 2997.709 Da / Num. of mol.: 1 / Mutation: P9A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (bacteria) / Strain: 168 / Gene: spoVM, BSU15810 / Plasmid: pKR209 / Production host: Escherichia coli (E. coli) / References: UniProt: P37817

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1212D 1H-13C HSQC
1313D HNCA
1413D HN(CA)CB
1513D HN(CO)CA
1613D 1H-15N NOESY
1713D 1H-13C NOESY
1813D (H)CCH-TOCSY
1913D HNCO

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Sample preparation

DetailsContents: 0.5-1 mM [U-100% 13C; U-100% 15N] protein, 16 mM sodium phosphate, 80 mM sodium chloride, 95% H2O/5% D2O
Solvent system: 95% H2O/5% D2O
Sample
Conc. (mg/ml)UnitsComponentIsotopic labelingConc. range (mg/ml)Solution-ID
mMprotein-1[U-100% 13C; U-100% 15N]0.5-11
16 mMsodium phosphate-21
80 mMsodium chloride-31
Sample conditionsIonic strength: 80 / pH: 6.0 / Pressure: ambient / Temperature: 310 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AvanceBrukerAVANCE8501
Bruker AvanceBrukerAVANCE6002

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Processing

NMR software
NameDeveloperClassification
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
NMRViewJohnson, One Moon Scientificdata analysis
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorerefinement
CYANAGuntert, Mumenthaler and Wuthrichstructure solution
RefinementMethod: simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 50 / Conformers submitted total number: 10

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