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- PDB-2k3c: Structural and Functional Characterization of TM IX of the NHE1 I... -

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Basic information

Entry
Database: PDB / ID: 2k3c
TitleStructural and Functional Characterization of TM IX of the NHE1 Isoform of the Na+/H+ Exchanger
ComponentsTMIX peptide
KeywordsMETAL TRANSPORT / membrane peptide / dodecylphosphocholine micelle / NHE1 / Na+/H+ transporter
MethodSOLUTION NMR / simulated annealing
Model details31 residue peptide in dodecylphosphocholine micelles
AuthorsReddy, T. / Ding, J. / Li, X. / Sykes, B.D. / Fliegel, L. / Rainey, J.K.
CitationJournal: J.Biol.Chem. / Year: 2008
Title: Structural and Functional Characterization of Transmembrane Segment IX of the NHE1 Isoform of the Na+/H+ Exchanger.
Authors: Reddy, T. / Ding, J. / Li, X. / Sykes, B.D. / Rainey, J.K. / Fliegel, L.
History
DepositionMay 1, 2008Deposition site: BMRB / Processing site: RCSB
Revision 1.0Jun 3, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 19, 2020Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_software / pdbx_struct_assembly / pdbx_struct_oper_list / struct_conn
Item: _pdbx_database_status.status_code_cs / _pdbx_nmr_software.name / _struct_conn.pdbx_leaving_atom_flag
Revision 1.3Nov 27, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: TMIX peptide


Theoretical massNumber of molelcules
Total (without water)3,4421
Polymers3,4421
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)40 / 100structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein/peptide TMIX peptide


Mass: 3442.213 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: solid-phase peptide synthesis
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
Details: 31 residue peptide in dodecylphosphocholine micelles
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-13C HSQC
1212D 1H-1H TOCSY
1312D 1H-1H NOESY

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Sample preparation

DetailsContents: 0.8-1.0 mM TMIX peptide, 95% H2O/5% D2O / Solvent system: 95% H2O/5% D2O
SampleConc.: 0.8 mM / Component: TMIX peptide
Sample conditionspH: 5.05 / Pressure: ambient / Temperature: 303.15 K

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NMR measurement

NMR spectrometerType: Varian INOVA / Manufacturer: Varian / Model: INOVA / Field strength: 800 MHz

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Processing

NMR software
NameVersionDeveloperClassification
X-PLOR NIH2.18Schwieters, Kuszewski, Tjandra and Clorestructure solution
Sparky3.112Goddardpeak picking
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
NMRDrawDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
X-PLOR NIH2.18Schwieters, Kuszewski, Tjandra and Clorerefinement
RefinementMethod: simulated annealing / Software ordinal: 1
Details: 21 rounds of structural refinement in XPLOR-NIH by simulated annealing, then an additional 6 rounds were performed with dihedral angle potential scaling factors of 5, 50, 100, 100, 50 and 25. ...Details: 21 rounds of structural refinement in XPLOR-NIH by simulated annealing, then an additional 6 rounds were performed with dihedral angle potential scaling factors of 5, 50, 100, 100, 50 and 25. 15,000 cooling steps.
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 40

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