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- PDB-2ky4: Solution NMR structure of the PBS linker domain of phycobilisome ... -

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Basic information

Entry
Database: PDB / ID: 2ky4
TitleSolution NMR structure of the PBS linker domain of phycobilisome linker polypeptide from Anabaena sp. Northeast Structural Genomics Consortium Target NsR123E
ComponentsPhycobilisome linker polypeptide
KeywordsPHOTOSYNTHESIS / NESG / PSI / Structural Genomics / Protein Structure Initiative / Northeast Structural Genomics Consortium
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 speciesNostoc sp. (bacteria)
MethodSOLUTION NMR / simulated annealing
Model detailslowest energy, model 1
AuthorsHe, Y. / Eletsky, A. / Mills, J.L. / Lee, D. / Ciccosanti, C. / Hamilton, K. / Acton, T.B. / Xiao, R. / Everett, J.K. / Lee, H. ...He, Y. / Eletsky, A. / Mills, J.L. / Lee, D. / Ciccosanti, C. / Hamilton, K. / Acton, T.B. / Xiao, R. / Everett, J.K. / Lee, H. / 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 linker polypeptide from Anabaena sp. Northeast Structural Genomics Consortium Target NsR123E
Authors: He, Y. / Eletsky, A. / Mills, J.L. / Lee, D. / Ciccosanti, C. / Hamilton, K. / Acton, T.B. / Xiao, R. / Everett, J.K. / Lee, H. / Montelione, G.T. / Szyperski, T.
History
DepositionMay 14, 2010Deposition site: BMRB / Processing site: RCSB
Revision 1.0Jul 14, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 16, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_nmr_spectrometer / pdbx_struct_assembly / pdbx_struct_oper_list / 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 linker polypeptide


Theoretical massNumber of molelcules
Total (without water)17,2551
Polymers17,2551
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)14 / 100target function
RepresentativeModel #1lowest energy

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Components

#1: Protein Phycobilisome linker polypeptide / Anchor polypeptide / PBS-anchor protein


Mass: 17254.598 Da / Num. of mol.: 1 / Fragment: PBS-linker 3 domain residues 727-867
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Nostoc sp. (bacteria) / Strain: PCC 7120 / Gene: alr0020, apcE / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)+ Magic / References: UniProt: P80559

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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 ali
1312D 1H-13C CT-HSQC aro
1422D 1H-13C CT-HSQC (methyl)
1513D HNCO
1613D HN(CA)CO
1713D CBCA(CO)NH
1813D HN(CA)CB
1913D (H)CCH-TOCSY
11013D (H)CCH-COSY ali
11113D (H)CCH-COSY aro
11213D HBHA(CO)NH
113113C/15N-NOESY
11432D J-modulation 1H-15N HSQC
11542D J-modulation 1H-15N HSQC
11622D J-modulation 1H-15N HSQC

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Sample preparation

Details
Solution-IDContentsSolvent system
10.95 mM [U-100% 13C; U-100% 15N] protein, 100 mM sodium chloride, 5 mM calcium chloride, 10 mM DTT, 20 mM MES, 0.02 % by volume NaN3, 50 uM DSS, 90% H2O/10% D2O90% H2O/10% D2O
20.975 mM [U-5% 13C; U-100% 15N] protein, 100 mM sodium chloride, 5 mM calcium chloride, 10 mM DTT, 20 mM MES, 0.02 % by volume NaN3, 50 uM DSS, 90% H2O/10% D2O90% H2O/10% D2O
30.664 mM [U-5% 13C; U-100% 15N] protein, 100 mM sodium chloride, 5 mM calcium chloride, 10 mM DTT, 20 mM MES, 0.02 % by volume NaN3, 50 uM DSS, 4 % by volume poly ethylene glycol, 82% H2O/18% D2O82% H2O/18% D2O
40.851 mM [U-5% 13C; U-100% 15N] protein, 100 mM sodium chloride, 5 mM calcium chloride, 10 mM DTT, 20 mM MES, 0.02 % by volume NaN3, 50 uM DSS, 7 % by volume poly acrylamide gel, 83% H2O/17% D2O83% H2O/17% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.95 mMprotein-1[U-100% 13C; U-100% 15N]1
100 mMsodium chloride-21
5 mMcalcium chloride-31
10 mMDTT-41
20 mMMES-51
0.02 %NaN3-61
50 uMDSS-71
0.975 mMprotein-8[U-5% 13C; U-100% 15N]2
100 mMsodium chloride-92
5 mMcalcium chloride-102
10 mMDTT-112
20 mMMES-122
0.02 %NaN3-132
50 uMDSS-142
0.664 mMprotein-15[U-5% 13C; U-100% 15N]3
100 mMsodium chloride-163
5 mMcalcium chloride-173
10 mMDTT-183
20 mMMES-193
0.02 %NaN3-203
50 uMDSS-213
4 %poly ethylene glycol-223
0.851 mMprotein-23[U-5% 13C; U-100% 15N]4
100 mMsodium chloride-244
5 mMcalcium chloride-254
10 mMDTT-264
20 mMMES-274
0.02 %NaN3-284
50 uMDSS-294
7 %poly acrylamide gel-304
Sample conditionsIonic strength: 117.5 / pH: 6.5 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian INOVAVarianINOVA7501
Varian INOVAVarianINOVA6002
Bruker AvanceBrukerAVANCE9003

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Processing

NMR software
NameVersionDeveloperClassification
VnmrJ2.1BVariancollection
NMRPipe2007.030.16.06Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
PROSA6.4Guntertprocessing
XEASYBartels et al.data analysis
AutoAssignZimmerman, Moseley, Kulikowski and Montelionechemical shift assignment
CYANA3Guntert, Mumenthaler and Wuthrichstructure solution
AutoStructure2.2.1Huang, Tejero, Powers and Montelionestructure solution
TALOS+1.2009.0721.18Shen, Cornilescu, Delaglio and Baxdata analysis
CARA1.8.4Keller and Wuthrichchemical shift assignment
CARA1.8.4Keller and Wuthrichpeak picking
CARA1.8.4Keller and Wuthrichdata analysis
CNS1.2.1Brunger, Adams, Clore, Gros, Nilges and Readrefinement
PSVS1.3Bhattacharya and Montelionevalidation
NMRDraw3Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxdata analysis
MOLMOLKoradi, Billeter and Wuthrichrefinement
TopSpin2.1Bruker Biospindata analysis
RefinementMethod: simulated annealing / Software ordinal: 1
Details: Structure determination was performed iteratively with CYANA v3.0 using NOE-based constraints, PHI and PSI dihedral angle constraints from TALOS+, and RDC constraints. The 20 conformers out ...Details: Structure determination was performed iteratively with CYANA v3.0 using NOE-based constraints, PHI and PSI dihedral angle constraints from TALOS+, and RDC constraints. 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.
NMR constraintsNOE constraints total: 3271 / NOE intraresidue total count: 525 / NOE long range total count: 782 / NOE medium range total count: 1120 / NOE sequential total count: 844
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 100 / Conformers submitted total number: 14

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