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- PDB-2mxa: Solution structure of the NDH-1 complex subunit CupS from Thermos... -

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Basic information

Entry
Database: PDB / ID: 2mxa
TitleSolution structure of the NDH-1 complex subunit CupS from Thermosynechococcus elongatus
ComponentsNDH-1 complex sensory subunit CupS
KeywordsMEMBRANE PROTEIN / Bioenergetics-electron transfer complex / Cyanobacteria / NDH-1 complex
Function / homologyFAS1 domain / FAS1 domain superfamily / Fasciclin domain / FAS1/BIgH3 domain profile. / Four repeated domains in the Fasciclin I family of proteins, present in many other contexts. / Tll0220 protein
Function and homology information
Biological speciesThermosynechococcus elongatus (bacteria)
MethodSOLUTION NMR / torsion angle dynamics
Model detailslowest energy, model5
AuthorsKorste, A. / Wulfhorst, H. / Ikegami, T. / Nowaczyk, M.M. / Stoll, R.
CitationJournal: Biochim.Biophys.Acta / Year: 2015
Title: Solution structure of the NDH-1 complex subunit CupS from Thermosynechococcus elongatus.
Authors: Korste, A. / Wulfhorst, H. / Ikegami, T. / Nowaczyk, M.M. / Stoll, R.
History
DepositionDec 17, 2014Deposition site: BMRB / Processing site: RCSB
Revision 1.0Jun 10, 2015Provider: repository / Type: Initial release
Revision 1.1Aug 26, 2015Group: Database references
Revision 1.2Jun 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 1.3May 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: NDH-1 complex sensory subunit CupS


Theoretical massNumber of molelcules
Total (without water)16,9851
Polymers16,9851
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 / 40structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein NDH-1 complex sensory subunit CupS


Mass: 16985.387 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermosynechococcus elongatus (bacteria)
Gene: CupS / Production host: Escherichia coli (E. coli) / References: UniProt: Q8DMA1

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC/HMQC
1212D 1H-13C HSQC/HMQC
1313D HN(CA)CB
1413D CBCA(CO)NH
1513D 1H-15N NOESY
1613D HBHA(CO)NH
1713D H(CCO)NH
1813D C(CO)NH
1913D HNCO
11013D (H)CCH-TOCSY
11113D (H)CCH-COSY
11213D 1H-13C NOESY aliphatic
11313D 1H-13C NOESY aromatic

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Sample preparation

DetailsContents: 0.5 mM [U-99% 13C; U-99% 15N] CupS, 50 mM Tris, 50 mM NaCl, 10 mM [U-2H] DTT, 90% H2O/10% D2O
Solvent system: 90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.5 mMCupS-1[U-99% 13C; U-99% 15N]1
50 mMTris-21
50 mMNaCl-31
10 mMDTT-4[U-2H]1
Sample conditionspH: 8.0 / Pressure: 1 atm / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AvanceBrukerAVANCE9501
Bruker DRXBrukerDRX5002
Bruker DRXBrukerDRX6003
Bruker AvanceBrukerAVANCE8004

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Processing

NMR software
NameVersionDeveloperClassification
CcpNmr Analysis2.2CCPNspectrum analysis
NMRDrawanyDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxspectrum display
NMRPipeanyDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxspectrum processing
NMRPipeanyDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxstructure solution
NMRPipeanyLinge, O'Donoghue and Nilgesspectrum processing
NMRPipeanyLinge, O'Donoghue and Nilgesstructure solution
CNSBrunger, Adams, Clore, Gros, Nilges and Readstructure solution
TALOSCornilescu, Delaglio and Baxdata analysis
TALOSCornilescu, Delaglio and Baxstructure solution
TALOSLinge, O'Donoghue and Nilgesdata analysis
TALOSLinge, O'Donoghue and Nilgesstructure solution
TALOSCornilescu, Delaglio and Baxdata analysis
TALOSCornilescu, Delaglio and Baxstructure solution
TALOSLinge, O'Donoghue and Nilgesdata analysis
TALOSLinge, O'Donoghue and Nilgesstructure solution
ARIArefinement
RefinementMethod: torsion angle dynamics / Software ordinal: 1 / Details: including water refinement
NMR constraintsNOE constraints total: 2089 / NOE intraresidue total count: 929 / NOE long range total count: 431 / NOE medium range total count: 281 / NOE sequential total count: 448
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 40 / Conformers submitted total number: 10

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