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- PDB-2h3o: Structure of MERFT, a membrane protein with two trans-membrane helices -

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Basic information

Entry
Database: PDB / ID: 2h3o
TitleStructure of MERFT, a membrane protein with two trans-membrane helices
ComponentsMerF
KeywordsMEMBRANE PROTEIN / ALPHA-HELIX / BICELLE
Function / homologybacterial mercury transporter, merf / Mercury ion transport, MerF / Membrane transport protein MerF / Helix Hairpins / Orthogonal Bundle / Mainly Alpha / membrane / MerF
Function and homology information
Biological speciesMorganella morganii (bacteria)
MethodSOLID-STATE NMR / DIRECT STRUCTURAL FITTING OF 2D SOLID-STATE NMR DATA
AuthorsOpella, S.J. / De Angelis, A.A. / Howell, S.C. / Nevzorov, A.A.
CitationJournal: J.Am.Chem.Soc. / Year: 2006
Title: Structure Determination of a Membrane Protein with Two Trans-membrane Helices in Aligned Phospholipid Bicelles by Solid-State NMR Spectroscopy.
Authors: De Angelis, A.A. / Howell, S.C. / Nevzorov, A.A. / Opella, S.J.
History
DepositionMay 22, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 3, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 20, 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 1.4May 29, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond
Remark 999SEQUENCE Residue at position 72 is a C72S mutation. Residue Ser is further modified to Homoserine

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Structure visualization

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Assembly

Deposited unit
A: MerF


Theoretical massNumber of molelcules
Total (without water)6,4091
Polymers6,4091
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)1 / 20structures with the least restraint violations
Representative

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Components

#1: Protein MerF


Mass: 6408.632 Da / Num. of mol.: 1 / Fragment: Helix-loop-helix, residues 12-72 / Mutation: C21S, C22S, C71S, C72(GLX)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Morganella morganii (bacteria) / Gene: merF / Plasmid: PET31B-MERFT / Production host: Escherichia coli (E. coli) / Strain (production host): C43(DE3) / References: UniProt: Q56446

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Experimental details

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Experiment

ExperimentMethod: SOLID-STATE NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
111PISEMA
121SAMMY
NMR detailsText: 15N chemical shifts and 1H-15N dipolar couplings were measured by solid-state NMR

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Sample preparation

DetailsContents: 6 mM MerFt aligned in large 14-O-PC/6-O-PC phospholipid bicelles, 28% (w/v) in H2O
Solvent system: H2O
Sample conditionspH: 5 / Pressure: ambient / Temperature: 313 K

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometerType: Bruker AVANCE / Manufacturer: Bruker / Model: AVANCE / Field strength: 700 MHz

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Processing

NMR software
NameVersionDeveloperClassification
NMRPipe2.3Delaglio, F et al.data analysis
Sparky3.11Goddard, T.D. et al.data analysis
Structural Fitting2Nevzorov, A.A and Opella, S.J.refinement
RefinementMethod: DIRECT STRUCTURAL FITTING OF 2D SOLID-STATE NMR DATA
Software ordinal: 1
Details: This structure was calculated by using a structural fitting algorithm that finds torsion angles between consecutive residues based on their 15N chemical shift, 1H-15N dipolar coupling ...Details: This structure was calculated by using a structural fitting algorithm that finds torsion angles between consecutive residues based on their 15N chemical shift, 1H-15N dipolar coupling frequencies and Ramachandran maps. One hydrophobic matching and one loose helix-helix distance restraints were used
NMR ensembleConformer selection criteria: structures with the least restraint violations
Conformers calculated total number: 20 / Conformers submitted total number: 1

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