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- PDB-2l06: Solution NMR structure of the PBS linker polypeptide domain (frag... -

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Basic information

Entry
Database: PDB / ID: 2l06
TitleSolution NMR structure of the PBS linker polypeptide domain (fragment 254-400) of phycobilisome linker protein ApcE from Synechocystis sp. PCC 6803. Northeast Structural Genomics Consortium Target SgR209C
ComponentsPhycobilisome LCM core-membrane linker polypeptide
KeywordsPROTEIN BINDING / alpha / Structural Genomics / PSI-2 / Protein Structure Initiative / Northeast Structural Genomics Consortium / NESG
Function / homology
Function and homology information


Lyases / phycobilisome / plasma membrane-derived thylakoid membrane / photosynthesis / lyase activity
Similarity search - Function
Phycobilisome linker domain / serine acetyltransferase, domain 1 / Phycobilisome linker domain / Phycobilisome linker domain superfamily / Phycobilisome Linker polypeptide / Phycobilisome (PBS) linker domain profile. / Phycobilisome, alpha/beta subunit / Phycobilisome, alpha/beta subunit superfamily / Phycobilisome protein / Globin-like superfamily ...Phycobilisome linker domain / serine acetyltransferase, domain 1 / Phycobilisome linker domain / Phycobilisome linker domain superfamily / Phycobilisome Linker polypeptide / Phycobilisome (PBS) linker domain profile. / Phycobilisome, alpha/beta subunit / Phycobilisome, alpha/beta subunit superfamily / Phycobilisome protein / Globin-like superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Phycobiliprotein ApcE
Similarity search - Component
Biological speciesSynechocystis sp. (bacteria)
MethodSOLUTION NMR / simulated annealing
AuthorsRamelot, T.A. / Yang, Y. / Cort, J.R. / Hamilton, K. / Ciccosanti, C. / Lee, D. / Acton, T.B. / Xiao, R. / Everett, J.K. / Montelione, G.T. ...Ramelot, T.A. / Yang, Y. / Cort, J.R. / Hamilton, K. / Ciccosanti, C. / Lee, D. / 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 PBS linker polypeptide domain of phycobilisome linker protein apcE from Synechocystis sp. Northeast Structural Genomics Consortium Target SgR209C
Authors: Ramelot, T.A. / Yang, Y. / Cort, J.R. / Hamilton, K. / Ciccosanti, C. / Lee, D. / Acton, T.B. / Xiao, R. / Everett, J.K. / Montelione, G.T. / Kennedy, M.A.
History
DepositionJun 30, 2010Deposition site: BMRB / Processing site: RCSB
Revision 1.0Aug 25, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.2Feb 5, 2020Group: 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: _pdbx_database_status.status_code_cs / _pdbx_nmr_software.name ..._pdbx_database_status.status_code_cs / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model / _struct_ref_seq_dif.details
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 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 LCM core-membrane linker polypeptide


Theoretical massNumber of molelcules
Total (without water)17,8681
Polymers17,8681
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)20 / 125structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Phycobilisome LCM core-membrane linker polypeptide


Mass: 17868.236 Da / Num. of mol.: 1 / Fragment: sequence database residues 254-401
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Synechocystis sp. (bacteria) / Strain: PCC 6803 / Gene: apcE, slr0335 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) pMGK / References: UniProt: Q55544

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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
1313D 1H-15N NOESY
1413D 1H-13C NOESY aliph
1524D 1H-13C NOESY
1613D HNCO
1713D CBCA(CO)NH
1813D HN(CA)CB
1913D (H)CC(CO)NH-TOCSY
11023D (H)CCH-TOCSY
11123D (H)CCH-COSY
11222D 1H-15N HSQC
11332D 1H-13C HSQC
11413D H(CC)(CO)NH-TOCSY
11513D 1H-13C NOESY arom
1162(H)CCH-TOCSY
11713D HNCA
11813D HN(CO)CA

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Sample preparation

Details
Solution-IDContentsSolvent system
120 mM MES, 100 mM sodium chloride, 5 mM calcium chloride, 100 mM DTT, 0.02 % sodium azide, 1.4 mM [U-100% 13C; U-100% 15N] protein, 95% H2O/5% D2O95% H2O/5% D2O
220 mM MES, 100 mM sodium chloride, 5 mM calcium chloride, 100 mM DTT, 0.02 % sodium azide, 1.4 mM [U-100% 13C; U-100% 15N] protein, 100% D2O100% D2O
320 mM MES, 100 mM sodium chloride, 5 mM calcium chloride, 100 mM DTT, 0.02 % sodium azide, 1.2 mM [U-5% 13C; U-100% 15N] protein, 95% H2O/5% D2O95% H2O/5% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
20 mMMES1
100 mMsodium chloride1
5 mMcalcium chloride1
100 mMDTT1
0.02 %sodium azide1
1.4 mMprotein[U-100% 13C; U-100% 15N]1
20 mMMES2
100 mMsodium chloride2
5 mMcalcium chloride2
100 mMDTT2
0.02 %sodium azide2
1.4 mMprotein[U-100% 13C; U-100% 15N]2
20 mMMES3
100 mMsodium chloride3
5 mMcalcium chloride3
100 mMDTT3
0.02 %sodium azide3
1.2 mMprotein[U-5% 13C; U-100% 15N]3
Sample conditionsIonic strength: 100 / pH: 6.5 / Pressure: ambient / Temperature: 293 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian INOVAVarianINOVA6001
Bruker AvanceIIIBrukerAVANCE III8502
Varian INOVAVarianINOVA5003
Varian INOVAVarianINOVA7504

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Processing

NMR software
NameVersionDeveloperClassification
NMRPipelinux9Delaglio, 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
Sparky3.113Goddarddata analysis
PSVS1.4Bhattacharya and Montelionestructure validation
AutoAssign2.3.0Zimmerman, Moseley, Kulikowski and Montelionechemical shift assignment
PdbStat5(PDBStat) R. Tejero, G.T. Montelionedata analysis
CYANA2.1Guntert, Mumenthaler and Wuthrichdata analysis
X-PLOR NIH2.25Schwieters, Kuszewski, Tjandra and Clorerefinement
RefinementMethod: simulated annealing / Software ordinal: 1 / Details: CNS water refinement
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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