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- PDB-2l3w: Solution NMR Structure of the PBS linker domain of phycobilisome ... -

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Basic information

Entry
Database: PDB / ID: 2l3w
TitleSolution NMR Structure of the PBS linker domain of phycobilisome rod linker polypeptide from Synechococcus elongatus, Northeast Structural Genomics Consortium Target SnR168A
ComponentsPhycobilisome rod linker polypeptide
KeywordsPHOTOSYNTHESIS / Structural Genomics / NORTHEAST STRUCTURAL GENOMICS CONSORTIUM (NESG) / PSI-Biology / Protein Structure Initiative
Function / homology
Function and homology information


phycobilisome / 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 rod linker polypeptide
Similarity search - Component
Biological speciesSynechococcus elongatus (bacteria)
MethodSOLUTION NMR / simulated annealing
Model detailslowest energy, model 1
AuthorsEletsky, A. / Lee, H. / Lee, D. / Ciccosanti, C. / Hamilton, K. / Acton, T.B. / Xiao, R. / Everett, J.K. / Prestegard, J.H. / Montelione, G.T. ...Eletsky, A. / Lee, H. / Lee, D. / Ciccosanti, C. / Hamilton, K. / Acton, T.B. / Xiao, R. / Everett, J.K. / Prestegard, J.H. / Montelione, G.T. / Szyperski, T. / Northeast Structural Genomics Consortium (NESG)
CitationJournal: To be Published
Title: Solution NMR Structure of the PBS linker domain of phycobilisome rod linker polypeptide from Synechococcus elongatus, Northeast Structural Genomics Consortium Target SnR168A
Authors: Eletsky, A. / Lee, H. / Lee, D. / Ciccosanti, C. / Hamilton, K. / Acton, T.B. / Xiao, R. / Everett, J.K. / Prestegard, J.H. / Montelione, G.T. / Szyperski, T.
History
DepositionSep 24, 2010Deposition site: BMRB / Processing site: RCSB
Revision 1.0Dec 15, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 22, 2012Group: Structure summary
Revision 1.3May 1, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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_nmr_software.name / _pdbx_nmr_spectrometer.model / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Phycobilisome rod linker polypeptide


Theoretical massNumber of molelcules
Total (without water)16,4261
Polymers16,4261
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 / 100structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Phycobilisome rod linker polypeptide


Mass: 16426.092 Da / Num. of mol.: 1 / Fragment: sequence database residues 20-153
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Synechococcus elongatus (bacteria) / Strain: PCC 7942 / Gene: Synpcc7942_1049 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)+ Magic / References: UniProt: Q31PE0

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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 CT-HSQC aliphatic
1312D 1H-13C CT-HSQC aromatic
1412D 1H-13C HSQC aliphatic
1513D HN(CA)CB
1613D HNCO
1713D simutaneous 13C-aromatic,13C-aliphatic,15N edited 1H-1H NOESY
1813D HN(CA)CO
1913D CBCA(CO)NH
11013D HBHA(CO)NH
11113D (H)CCH-COSY aliphatic
11213D (H)CCH-COSY aromatic
11313D (H)CCH-TOCSY
11412D 1H-15N LR-HSQC (Histidine)
11511D 1H-15N HSQC T1
11611D 1H-15N HSQC T2
11722D 1H-13C CT-HSQC (methyl)
11822D 1H-15N J-MODULATED HSQC
11932D 1H-15N J-MODULATED HSQC
12042D 1H-15N J-MODULATED HSQC

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Sample preparation

Details
Solution-IDContentsSolvent system
10.9 mM [U-100% 13C; U-100% 15N] SnR168A, 20 mM MES, 100 mM sodium chloride, 5 mM calcium chloride, 10 mM DTT, 0.02 % sodium azide, 90% H2O/10% D2O90% H2O/10% D2O
20.7 mM [5% 13C; U-100% 15N] SnR168A, 20 mM MES, 100 mM sodium chloride, 5 mM calcium chloride, 10 mM DTT, 0.02 % sodium azide, 90% H2O/10% D2O90% H2O/10% D2O
30.45 mM [5% 13C; U-100% 15N] SnR168A, 13 mM MES, 160 mM sodium chloride, 3.2 mM calcium chloride, 6.4 mM DTT, 0.025 % sodium azide, 2.4 mM potassium phosphate, 0.5 mM magnesium chloride, 13.2 g/l Pf1 phage, 85% H2O/15% D2O85% H2O/15% D2O
40.46 mM [5% 13C; U-100% 15N] SnR168A, 18 mM MES, 90 mM sodium chloride, 4.5 mM calcium chloride, 9 mM DTT, 0.02 % sodium azide, 4 % C12E5 PEG, 4 % hexanol, 85% H2O/15% D2O85% H2O/15% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.9 mMSnR168A-1[U-100% 13C; U-100% 15N]1
20 mMMES-21
100 mMsodium chloride-31
5 mMcalcium chloride-41
10 mMDTT-51
0.02 %sodium azide-61
0.7 mMSnR168A-7[5% 13C; U-100% 15N]2
20 mMMES-82
100 mMsodium chloride-92
5 mMcalcium chloride-102
10 mMDTT-112
0.02 %sodium azide-122
0.45 mMSnR168A-13[5% 13C; U-100% 15N]3
13 mMMES-143
160 mMsodium chloride-153
3.2 mMcalcium chloride-163
6.4 mMDTT-173
0.025 %sodium azide-183
2.4 mMpotassium phosphate-193
0.5 mMmagnesium chloride-203
13.2 mg/mLPf1 phage-213
0.46 mMSnR168A-22[5% 13C; U-100% 15N]4
18 mMMES-234
90 mMsodium chloride-244
4.5 mMcalcium chloride-254
9 mMDTT-264
0.02 %sodium azide-274
4 %C12E5 PEG-284
4 %hexanol-294
Sample conditionspH: 6.5 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AvanceBrukerAVANCE9001
Varian INOVAVarianINOVA7502
Bruker AvanceBrukerAVANCE7003
Varian INOVAVarianINOVA6004
Varian INOVAVarianINOVA5005

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Processing

NMR software
NameVersionDeveloperClassification
CNS1.2Brunger, Adams, Clore, Gros, Nilges and Readrefinement
CNS1.2Brunger, Adams, Clore, Gros, Nilges and Readstructure solution
CNS1.2Brunger, Adams, Clore, Gros, Nilges and Readgeometry optimization
CYANA3Guntert, Mumenthaler and Wuthrichrefinement
CYANA3Guntert, Mumenthaler and Wuthrichgeometry optimization
CYANA3Guntert, Mumenthaler and Wuthrichstructure solution
AutoStructure2.2.1Huang, Tejero, Powers and Montelionestructure solution
AutoStructure2.2.1Huang, Tejero, Powers and Montelionedata analysis
AutoAssign2.3.0Zimmerman, Moseley, Kulikowski and Montelionedata analysis
AutoAssign2.3.0Zimmerman, Moseley, Kulikowski and Montelionechemical shift assignment
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
XEASYBartels et al.data analysis
TopSpinBruker Biospincollection
TopSpinBruker Biospinprocessing
VnmrJVariancollection
CARA1.8.4Keller and Wuthrichdata analysis
CARA1.8.4Keller and Wuthrichchemical shift assignment
CARA1.8.4Keller and Wuthrichpeak picking
TALOS+Shen, Cornilescu, Delaglio and Baxgeometry optimization
PROSA6.4Guntertprocessing
RefinementMethod: simulated annealing / Software ordinal: 1
Details: Structure determination was performed by running CYANA and AUTOSTRUCTURE in parallel using NOE-based constraints and PHI and PSI dihedral angle constraints from TALOS+. Consensus peak ...Details: Structure determination was performed by running CYANA and AUTOSTRUCTURE in parallel using NOE-based constraints and PHI and PSI dihedral angle constraints from TALOS+. Consensus peak assignments were selected and used in iterative refinement with CYANA, with RDC constraints added at later stages. The 20 conformers out of 100 with the lowest target function were further refined by simulated annealing in explicit water bath using the program CNS with PARAM19 force field and upper limit constraints relaxed by 5%
NMR constraintsNOE constraints total: 2778 / NOE intraresidue total count: 359 / NOE long range total count: 791 / NOE medium range total count: 939 / NOE sequential total count: 689 / Protein chi angle constraints total count: 0 / Protein other angle constraints total count: 0 / Protein phi angle constraints total count: 105 / Protein psi angle constraints total count: 105
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 20

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