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- PDB-2k37: CsmA -

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Basic information

Entry
Database: PDB / ID: 2k37
TitleCsmA
ComponentsChlorosome Protein A
KeywordsPHOTOSYNTHESIS / PROTEIN / Bacteriochlorophyll / Chlorophyll / Chlorosome / Chromophore / Electron transport / Magnesium / Metal-binding / Transport
Function / homology
Function and homology information


chlorosome envelope / bacteriochlorophyll binding / photosynthesis / metal ion binding
Similarity search - Function
bacteriochlorophyll c-binding protein / Bacteriochlorophyll c-binding protein / Bacteriochlorophyll c-binding superfamily / Bacteriochlorophyll C binding protein / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Bacteriochlorophyll c-binding protein
Similarity search - Component
Biological speciesChlorobium tepidum (bacteria)
MethodSOLUTION NMR / simulated annealing
Model detailsSolution NMR structure of CsmA purified from 15-N labeled Chlorobium tepidum cells
AuthorsPedersen, M. / Dittmer, J. / Underhaug, J. / Miller, M. / Nielsen, N.C.
CitationJournal: Febs Lett. / Year: 2008
Title: The three-dimensional structure of CsmA: A small antenna protein from the green sulfur bacterium Chlorobium tepidum.
Authors: Pedersen, M.O. / Underhaug, J. / Dittmer, J. / Miller, M. / Nielsen, N.C.
History
DepositionApr 23, 2008Deposition site: BMRB / Processing site: RCSB
Revision 1.0Sep 2, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 19, 2020Group: Data collection / Derived calculations / Other
Category: pdbx_database_status / pdbx_nmr_software ...pdbx_database_status / pdbx_nmr_software / pdbx_nmr_spectrometer / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _pdbx_database_status.status_code_cs / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model
Revision 1.3Jun 14, 2023Group: Database references / Other / Category: database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data
Revision 1.4May 8, 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:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Chlorosome Protein A


Theoretical massNumber of molelcules
Total (without water)6,1601
Polymers6,1601
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)9 / 40structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Chlorosome Protein A / BACTERIOCHLOROPHYLL C-BINDING PROTEIN / BChl c-binding


Mass: 6160.034 Da / Num. of mol.: 1 / Fragment: residues 1-59 / Source method: isolated from a natural source / Source: (natural) Chlorobium tepidum (bacteria) / References: UniProt: P0A314

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
Details: Solution NMR structure of CsmA purified from 15-N labeled Chlorobium tepidum cells
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1212D 1H-1H TOCSY
1312D 1H-1H COSY
1412D 1H-1H NOESY
1513D HNHA
1613D NOESY-HSQC
1713D TOCSY-HSQC

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Sample preparation

DetailsContents: 1.4 mM [U-100% 15N] CsmA, 50% chloroform/50% methanol
Solvent system: 50% chloroform/50% methanol
SampleConc.: 1.4 mM / Component: CsmA / Isotopic labeling: [U-100% 15N]
Sample conditionsIonic strength: 0 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AvanceBrukerAVANCE8001
Bruker AvanceBrukerAVANCE7002

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Processing

NMR software
NameVersionDeveloperClassification
SparkyGoddardprocessing
TopSpinBrukercollection
ARIA2.2Linge, O'Donoghue and Nilgesstructure solution
ARIA2.2Linge, O'Donoghue and Nilgesrefinement
CNSBrunger, Adams, Clore, Gros, Nilges and Readrefinement
RefinementMethod: simulated annealing / Software ordinal: 1 / Details: CNS
NMR constraintsNOE constraints total: 1426 / NOE intraresidue total count: 490 / NOE long range total count: 0 / NOE medium range total count: 526 / NOE sequential total count: 338
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 40 / Conformers submitted total number: 9

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