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- PDB-1jo5: Rhodobacter sphaeroides Light Harvesting 1 beta Subunit in Deterg... -

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Basic information

Entry
Database: PDB / ID: 1jo5
TitleRhodobacter sphaeroides Light Harvesting 1 beta Subunit in Detergent Micelles
ComponentsLIGHT-HARVESTING PROTEIN B-875
KeywordsLUMINESCENT PROTEIN / helix-turn-helix / detergent micelle / membrane protein
Function / homology
Function and homology information


: / plasma membrane light-harvesting complex / bacteriochlorophyll binding / photosynthesis, light reaction / electron transporter, transferring electrons within the cyclic electron transport pathway of photosynthesis activity / membrane => GO:0016020 / metal ion binding / plasma membrane
Similarity search - Function
Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #250 / Antenna complex, beta subunit, conserved site / Antenna complexes beta subunits signature. / Antenna complex, beta domain superfamily / Light-harvesting protein B beta chain / Antenna complex, alpha/beta subunit / Light-harvesting complex / Antenna complex alpha/beta subunit / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Light-harvesting protein B-875 beta chain / Light-harvesting protein B-875 beta chain
Similarity search - Component
Biological speciesRhodobacter sphaeroides (bacteria)
MethodSOLUTION NMR
AuthorsSorgen, P.L. / Cahill, S.M. / Krueger-Koplin, R.D. / Krueger-Koplin, S.T. / Schenck, C.G. / Girvin, M.E.
CitationJournal: Biochemistry / Year: 2002
Title: Structure of the Rhodobacter sphaeroides light-harvesting 1 beta subunit in detergent micelles.
Authors: Sorgen, P.L. / Cahill, S.M. / Krueger-Koplin, R.D. / Krueger-Koplin, S.T. / Schenck, C.C. / Girvin, M.E.
History
DepositionJul 26, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 27, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 23, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name
Revision 1.4May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: LIGHT-HARVESTING PROTEIN B-875


Theoretical massNumber of molelcules
Total (without water)5,4611
Polymers5,4611
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/peptide LIGHT-HARVESTING PROTEIN B-875


Mass: 5461.166 Da / Num. of mol.: 1 / Fragment: BETA SUBUNIT / Source method: isolated from a natural source / Source: (natural) Rhodobacter sphaeroides (bacteria) / Strain: SK102 / References: UniProt: P02951, UniProt: P0C0Y1*PLUS

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 13C-separated NOESY
1213D 15N-separated NOESY
131HNHA
NMR detailsText: This structure was determined in 8% Zwittergent 3:12 detergent

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Sample preparation

DetailsContents: 1.7 mM LH1 beta subunit, 15N13C, 8% Zwittergent 3:12, 50mM phosphate buffer, pH 6.5, 310K, 90% H2O, 10% D2O
Solvent system: 90% H2O/10% D2O
Sample conditionsIonic strength: 50 mM Phosphate buffer / pH: 6.5 / Pressure: ambient / Temperature: 310 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometerType: Bruker DRX / Manufacturer: Bruker / Model: DRX / Field strength: 600 MHz

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Processing

NMR software
NameVersionDeveloperClassification
NMRView5.0.3Johnson and Blevinsdata analysis
NMRPipe1.8Delaglio et alprocessing
CNS1Brunger et alstructure solution
CNS1Brunger et alrefinement
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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