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- PDB-2l8v: Solution NMR structure of the phycobilisome linker polypeptide do... -

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Basic information

Entry
Database: PDB / ID: 2l8v
TitleSolution NMR structure of the phycobilisome linker polypeptide domain of CpcC (20-153) from Thermosynechococcus elongatus, Northeast Structural Genomics Consortium Target TeR219A
ComponentsPhycobilisome 32.1 kDa linker polypeptide, phycocyanin-associated, rod
KeywordsPHOTOSYNTHESIS / NESG / Structural Genomics / Northeast Structural Genomics Consortium / PSI-Biology
Function / homology
Function and homology information


phycobilisome / plasma membrane-derived thylakoid membrane / photosynthesis
Similarity search - Function
Phycobilisome linker domain / serine acetyltransferase, domain 1 / Phycobilisome linker protein / Phycobilisome linker domain / Phycobilisome linker domain superfamily / Phycobilisome Linker polypeptide / Phycobilisome (PBS) linker domain profile. / CpcD-like domain / CpcD/allophycocyanin linker domain / CpcD-like domain profile. ...Phycobilisome linker domain / serine acetyltransferase, domain 1 / Phycobilisome linker protein / Phycobilisome linker domain / Phycobilisome linker domain superfamily / Phycobilisome Linker polypeptide / Phycobilisome (PBS) linker domain profile. / CpcD-like domain / CpcD/allophycocyanin linker domain / CpcD-like domain profile. / CpcD/allophycocyanin linker domain / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Phycobilisome 32.1 kDa linker polypeptide, phycocyanin-associated, rod
Similarity search - Component
Biological speciesThermosynechococcus elongatus (bacteria)
MethodSOLUTION NMR / simulated annealing
Model detailslowest energy, model 1
AuthorsRamelot, T.A. / Yang, Y. / Cort, J.R. / Lee, D. / Ciccosanti, C. / Hamilton, K. / Acton, T.B. / Xiao, R. / Everett, J.K. / Montelione, G.T. ...Ramelot, T.A. / Yang, Y. / Cort, J.R. / Lee, D. / Ciccosanti, C. / Hamilton, K. / Acton, T.B. / Xiao, R. / Everett, J.K. / Montelione, G.T. / Kennedy, M.A. / Northeast Structural Genomics Consortium (NESG)
CitationJournal: To be Published
Title: Solution NMR structure of the phycobilisome linker polypeptide domain of CpcC (20-153) from Thermosynechococcus elongatus, Northeast Structural Genomics Consortium Target TeR219A
Authors: Ramelot, T.A. / Yang, Y. / Cort, J.R. / Lee, D. / Ciccosanti, C. / Hamilton, K. / Acton, T.B. / Xiao, R. / Everett, J.K. / Montelione, G.T. / Kennedy, M.A.
History
DepositionJan 26, 2011Deposition site: BMRB / Processing site: RCSB
Revision 1.0Feb 9, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
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:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Phycobilisome 32.1 kDa linker polypeptide, phycocyanin-associated, rod


Theoretical massNumber of molelcules
Total (without water)16,9071
Polymers16,9071
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)20 / 125structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Phycobilisome 32.1 kDa linker polypeptide, phycocyanin-associated, rod


Mass: 16906.799 Da / Num. of mol.: 1 / Fragment: sequence database residues 20-153
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermosynechococcus elongatus (bacteria)
Strain: BP-1 / Gene: cpcC, tlr1959 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) + Magic / References: UniProt: P50034

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1212D 1H-13C HSQC aliphatic
1312D 1H-13C HSQC aromatic
1432D 1H-15N HSQC
1522D 1H-13C HSQC-CT
1623D 1H-15N NOESY
1713D 1H-13C NOESY-aliph
1813D HNCO
1913D HN(CA)CB
11013D CBCA(CO)NH
11113D HN(CO)CA
11213D HBHA(CO)NH
11313D H(CCO)NH
11413D C(CCO)NH
11513D (H)CCH-COSY
11613D (H)CCH-TOCSY
11733D CCH-TOCSY
11834D CC-NOESY
11912D 1H-13C NOESY-aromatic

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Sample preparation

Details
Solution-IDContentsSolvent system
11.3 mM [U-100% 13C; U-100% 15N] protein, 10 mM Tris-HCl, 100 mM sodium chloride, 5 mM calcium chloride, 0.02 % sodium azide, 5 mM DTT, 90% H2O/10% D2O90% H2O/10% D2O
21.3 mM [U-5% 13C; U-100% 15N] protein, 10 mM Tris-HCl, 100 mM sodium chloride, 5 mM calcium chloride, 5 mM DTT, 0.02 % sodium azide, 90% H2O/10% D2O90% H2O/10% D2O
31.3 mM [U-100% 13C; U-100% 15N] protein, 10 mM Tris-HCl, 100 mM sodium chloride, 5 mM calcium chloride, 0.02 % sodium azide, 10 mM DTT, 100% D2O100% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1.3 mMprotein-1[U-100% 13C; U-100% 15N]1
10 mMTris-HCl-21
100 mMsodium chloride-31
5 mMcalcium chloride-41
0.02 %sodium azide-51
5 mMDTT-61
1.3 mMprotein-7[U-5% 13C; U-100% 15N]2
10 mMTris-HCl-82
100 mMsodium chloride-92
5 mMcalcium chloride-102
5 mMDTT-112
0.02 %sodium azide-122
1.3 mMprotein-13[U-100% 13C; U-100% 15N]3
10 mMTris-HCl-143
100 mMsodium chloride-153
5 mMcalcium chloride-163
0.02 %sodium azide-173
10 mMDTT-183
Sample conditionsIonic strength: 0.1 / pH: 7.5 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian INOVAVarianINOVA6001
Bruker Avance IIIBrukerAVANCE III8502

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Processing

NMR software
NameVersionDeveloperClassification
NMRPipe2008Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
VNMR6.1CVariancollection
TopSpin2.1.4Bruker Biospincollection
AutoStructure2.2.1Huang, Tejero, Powers and Montelionedata analysis
X-PLOR NIH2.25Schwieters, Kuszewski, Tjandra and Clorestructure solution
CNS1.2Brunger, Adams, Clore, Gros, Nilges and Readrefinement
Sparky3.113Goddarddata analysis
PSVS1.4Bhattacharya and Montelionerefinement
AutoAssign2.3Zimmerman, Moseley, Kulikowski and Montelionechemical shift assignment
PdbStat5.1(PdbStat)-Roberto Tejero and Gaetano T. Montelionestructure solution
PINE Server1Bahrami, Markley, Assadi, and Eghbalniachemical shift autoassignment
CYANA2.1Guntert, Mumenthaler and Wuthrichstructure solution
RefinementMethod: simulated annealing / Software ordinal: 1 / Details: CNS water refinement
NMR constraintsNOE constraints total: 1282 / NOE intraresidue total count: 329 / NOE long range total count: 324 / NOE medium range total count: 294 / NOE sequential total count: 335
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 125 / Conformers submitted total number: 20

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