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- PDB-2moz: Structure of the Membrane Protein MerF, a Bacterial Mercury Trans... -

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Basic information

Entry
Database: PDB / ID: 2moz
TitleStructure of the Membrane Protein MerF, a Bacterial Mercury Transporter, Improved by the Inclusion of Chemical Shift Anisotropy Constraints
ComponentsMerF
KeywordsMEMBRANE PROTEIN / Membrane Protein Structures by Solution NMR / MPSbyNMR / PSI-Biology / Structural Genomics
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)
MethodSOLUTION NMR / simulated annealing
Model detailslowest energy, model 1
AuthorsTian, Y. / Lu, G.J. / Marassi, F.M. / Opella, S.J. / Membrane Protein Structures by Solution NMR (MPSbyNMR)
CitationJournal: J.Biomol.Nmr / Year: 2014
Title: Structure of the membrane protein MerF, a bacterial mercury transporter, improved by the inclusion of chemical shift anisotropy constraints.
Authors: Tian, Y. / Lu, G.J. / Marassi, F.M. / Opella, S.J.
History
DepositionMay 7, 2014Deposition site: BMRB / Processing site: RCSB
Revision 1.0Jul 30, 2014Provider: repository / Type: Initial release
Revision 1.1Aug 27, 2014Group: Database references / Structure summary
Revision 1.2Sep 17, 2014Group: 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
Revision 1.4May 15, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 / Item: _database_2.pdbx_DOI

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Structure visualization

Structure viewerMolecule:
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Assembly

Deposited unit
A: MerF


Theoretical massNumber of molelcules
Total (without water)8,6701
Polymers8,6701
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)10 / 100structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein MerF


Mass: 8670.404 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Morganella morganii (bacteria) / Gene: merF / Production host: Escherichia coli (E. coli) / References: UniProt: Q56446
Sequence detailsTHE HOMOSERINE IS A RESULT OF THE CYANOGEN BROMIDE CLEAVAGE DURING PROTEIN PURIFICATION AND IS NOT ...THE HOMOSERINE IS A RESULT OF THE CYANOGEN BROMIDE CLEAVAGE DURING PROTEIN PURIFICATION AND IS NOT INCLUDED IN THE STRUCTURE CALCULATION.

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D DARR
1212D NC correlation
1313D HnNCa SLF
1413D HnNCo SLF
1513D HcCxCx SLF
2622D HETCOR
2723D HETCOR/SLF
282SAMPI4
292PISEMA

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Sample preparation

Details
Solution-IDContentsSolvent system
12.0-3.0 mM [U-99% 13C; U-99% 15N] protein, 10.0-15.0 mM DMPC, 100 % H2O, 100% H2O100% H2O
21.0-6.0 mg/mL [U-98% 15N] protein, 8 mg DHPC, 40 mg DMPC, 170 uL H2O, 100% H2O100% H2O
Sample
Conc. (mg/ml)UnitsComponentIsotopic labelingConc. range (mg/ml)Solution-ID
mMprotein-1[U-99% 13C; U-99% 15N]2.0-3.01
mMDMPC-210.0-15.01
100 %H2O-31
mg/mLprotein-4[U-98% 15N]1.0-6.02
8 mg/mLDHPC-52
40 mg/mLDMPC-62
170 uMH2O-72
Sample conditions
Conditions-IDpHPressure (kPa)Temperature (K)
16ambient 298 K
26ambient 315 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AvanceBrukerAVANCE7001
Varian DD2VarianDD28002

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Processing

NMR softwareName: X-PLOR NIH / Developer: Schwieters, Kuszewski, Tjandra and Clore / Classification: refinement
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: 10

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