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- PDB-1dx7: Light-harvesting complex 1 beta subunit from Rhodobacter sphaeroides -

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Basic information

Entry
Database: PDB / ID: 1dx7
TitleLight-harvesting complex 1 beta subunit from Rhodobacter sphaeroides
ComponentsLight harvesting 1 b(B850b) polypeptide
KeywordsLIGHT-HARVESTING PROTEIN / BACTERIOCHLOROPHYLL BINDING / MEMBRANE PROTEIN / LIGHT HARVESTING / PHOTOSYNTHESIS
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 / 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 / Antenna pigment protein beta chain
Similarity search - Component
Biological speciesRhodobacter sphaeroides (bacteria)
MethodSOLUTION NMR / distance geometry
AuthorsConroy, M.J. / Westerhuis, W. / Parkes-Loach, P.S. / Loach, P.A. / Hunter, C.N. / Williamson, M.P.
CitationJournal: J.Mol.Biol. / Year: 2000
Title: The Solution Structure of Rhodobacter Sphaeroides Lh1 B Reveals Two Helical Domains Separated by a Flexible Region: Structural Consequences for the Lh1 Complex
Authors: Conroy, M.J. / Westerhuis, W. / Parkes-Loach, P.S. / Loach, P.A. / Hunter, C.N. / Williamson, M.P.
History
DepositionDec 21, 1999Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 18, 2000Provider: repository / Type: Initial release
Revision 1.1May 7, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Sep 25, 2019Group: Data collection / Database references ...Data collection / Database references / Other / Source and taxonomy / Structure summary
Category: entity / entity_name_com ...entity / entity_name_com / entity_src_gen / pdbx_database_status / pdbx_nmr_software / struct_ref / struct_ref_seq
Item: _entity.pdbx_description / _entity_name_com.name ..._entity.pdbx_description / _entity_name_com.name / _entity_src_gen.pdbx_beg_seq_num / _entity_src_gen.pdbx_end_seq_num / _entity_src_gen.pdbx_gene_src_gene / _entity_src_gen.pdbx_gene_src_scientific_name / _entity_src_gen.pdbx_seq_type / _pdbx_database_status.status_code_mr / _pdbx_nmr_software.name / _struct_ref.db_code / _struct_ref.pdbx_align_begin / _struct_ref.pdbx_db_accession / _struct_ref.pdbx_seq_one_letter_code / _struct_ref_seq.db_align_beg / _struct_ref_seq.db_align_end / _struct_ref_seq.pdbx_db_accession
Revision 1.4May 15, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Light harvesting 1 b(B850b) polypeptide


Theoretical massNumber of molelcules
Total (without water)5,4611
Polymers5,4611
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)6 / 30LOWEST ENERGY
Representative

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Components

#1: Protein/peptide Light harvesting 1 b(B850b) polypeptide / Light-harvesting protein


Mass: 5461.166 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhodobacter sphaeroides (bacteria) / Cellular location: MEMBRANEBiological membrane / Gene: pufB, EBL86_10065 / Cellular location (production host): MEMBRANE / Production host: RHODOBACTER SPHAEROIDES (bacteria) / References: UniProt: Q7B300, UniProt: P0C0Y1*PLUS

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
111COSY
121NOESY
131TOCSY
NMR detailsText: SOLVENT: 1:1 CHLOROFORM-D:METHANOL-D3

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Sample preparation

Sample conditionsTemperature: 293 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

NMR spectrometerType: Bruker DRX / Manufacturer: Bruker / Model: DRX / Field strength: 500 MHz

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Processing

NMR software
NameVersionDeveloperClassification
X-PLOR3.1FBRUNGERrefinement
X-PLORstructure solution
RefinementMethod: distance geometry / Software ordinal: 1
NMR ensembleConformer selection criteria: LOWEST ENERGY / Conformers calculated total number: 30 / Conformers submitted total number: 6

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