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- PDB-2kix: Channel domain of BM2 protein from influenza B virus -

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Basic information

Entry
Database: PDB / ID: 2kix
TitleChannel domain of BM2 protein from influenza B virus
ComponentsBM2 protein
KeywordsTRANSPORT PROTEIN / BM2 / influenza B / channel
Function / homologyInfluenza B matrix protein 2 / Influenza B matrix protein 2 (BM2) / proton transmembrane transport / host cell plasma membrane / virion membrane / plasma membrane / Matrix protein 2
Function and homology information
Biological speciesInfluenza B virus
MethodSOLUTION NMR / simulated annealing
AuthorsWang, J. / Pielak, R. / McClintock, M. / Chou, J.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2009
Title: Solution structure and functional analysis of the influenza B proton channel.
Authors: Wang, J. / Pielak, R.M. / McClintock, M.A. / Chou, J.J.
History
DepositionMay 12, 2009Deposition site: BMRB / Processing site: RCSB
Revision 1.0Nov 10, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 13, 2021Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_nmr_spectrometer / pdbx_struct_assembly / pdbx_struct_oper_list / struct_ref_seq_dif
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 / _struct_ref_seq_dif.details
Revision 1.3May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: BM2 protein
B: BM2 protein
C: BM2 protein
D: BM2 protein


Theoretical massNumber of molelcules
Total (without water)15,3184
Polymers15,3184
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)15 / 100structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein/peptide
BM2 protein


Mass: 3829.557 Da / Num. of mol.: 4 / Fragment: residues 1-33 / Mutation: C11S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Influenza B virus (B/Taiwan/70061/2006)
Gene: BM2 / Production host: Escherichia coli (E. coli) / References: UniProt: B4UQM4

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1122D 1H-15N HSQC
1213D 1H-15N NOESY
1313D 1H-13C NOESY
1433D HNCA
1533D HN(CA)CB
1633D HNCO

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Sample preparation

Details
Solution-IDContentsSolvent system
10.8 mM [U-100% 15N] BM2, 250 mM dihexanoylphosphocholine, 40 mM sodium phosphate, 93% H2O/7% D2O93% H2O/7% D2O
20.8 mM [U-100% 13C; U-100% 15N] BM2, 250 mM [U-100% 2H] dihexanoylphosphocholine, 40 mM sodium phosphate, 93% H2O/7% D2O93% H2O/7% D2O
30.8 mM [U-100% 13C; U-100% 15N; U-80% 2H] BM2, 250 mM dihexanoylphosphocholine, 40 mM sodium phosphate, 93% H2O/7% D2O93% H2O/7% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.8 mMBM2[U-100% 15N]1
250 mMdihexanoylphosphocholine1
40 mMsodium phosphate1
0.8 mMBM2[U-100% 13C; U-100% 15N]2
250 mMdihexanoylphosphocholine[U-100% 2H]2
40 mMsodium phosphate2
0.8 mMBM2[U-100% 13C; U-100% 15N; U-80% 2H]3
250 mMdihexanoylphosphocholine3
40 mMsodium phosphate3
Sample conditionsIonic strength: 40 / pH: 7.5 / Pressure: ambient / Temperature: 305 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AvanceBrukerAVANCE6001
Bruker AvanceBrukerAVANCE7502

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Processing

NMR software
NameDeveloperClassification
X-PLOR NIHSchwieters, C.D. et al.refinement
NMRPipeDelaglio, F. et al.processing
NMRDrawDelaglio, F. et al.data analysis
XwinNMRBruker Biospincollection
TALOSCornilescu, G. et al.chemical shift calculation
ProcheckNMRLaskowski, R. et al.structure solution
CARAKeller, R. et al.chemical shift assignment
RefinementMethod: simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 15

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