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- PDB-2fft: NMR structure of Spinach Thylakoid Soluble Phosphoprotein of 9 kD... -

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Basic information

Entry
Database: PDB / ID: 2fft
TitleNMR structure of Spinach Thylakoid Soluble Phosphoprotein of 9 kDa in SDS Micelles
Componentsthylakoid soluble phosphoprotein
KeywordsPLANT PROTEIN / Thylakoid Soluble Phosphoprotein / TSP9 / Structural Genomics / PSI / Protein Structure Initiative / Center for Eukaryotic Structural Genomics / CESG
Function / homology
Function and homology information


PSII associated light-harvesting complex II binding / chloroplast photosystem I binding / chloroplast photosystem II binding / thylakoid membrane / response to light stimulus / chloroplast / lipid binding
Similarity search - Function
Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #930 / Thylakoid soluble phosphoprotein TSP9 / Thylakoid soluble phosphoprotein TSP9 superfamily / Thylakoid soluble phosphoprotein TSP9 / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Helix non-globular / Special
Similarity search - Domain/homology
: / Thylakoid soluble phosphoprotein
Similarity search - Component
Biological speciesSpinacia oleracea (spinach)
MethodSOLUTION NMR / torsion angle dynamics,simulated annealing
AuthorsSong, J. / Carlberg, I. / Lee, M.S. / Markley, J.L. / Center for Eukaryotic Structural Genomics (CESG)
CitationJournal: Biochemistry / Year: 2006
Title: Micelle-induced folding of spinach thylakoid soluble phosphoprotein of 9 kDa and its functional implications.
Authors: Song, J. / Lee, M.S. / Carlberg, I. / Vener, A.V. / Markley, J.L.
History
DepositionDec 20, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 17, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 9, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / 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 / _struct_ref_seq_dif.details
Revision 1.4May 29, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: thylakoid soluble phosphoprotein


Theoretical massNumber of molelcules
Total (without water)8,7431
Polymers8,7431
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 / 100target function
RepresentativeModel #1lowest energy

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Components

#1: Protein thylakoid soluble phosphoprotein


Mass: 8742.819 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Spinacia oleracea (spinach) / Gene: TSP9 / Plasmid: PVP13 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: GenBank: 27529048, UniProt: Q8GT36*PLUS

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1111H,15N-HSQC
1211H,13C-HSQC
131HN(CA)CB
1411H,13C-HSQC
151CBCA(CO)NH
161C(CO)NH
171HCCHTOCSY
181HBACONH
19113C-EDITED 1H,1H-NOESY
110115C-EDITED 1H,1H-NOESY
NMR detailsText: ALL TRIPLE-RESONANCE AND NOESY SPECTRA WERE ACQUIRED USING THE SPECTROMETERS EQUIPPED WITH A CRYOGENIC PROBE.

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Sample preparation

DetailsContents: 10 mM HEPES, 100mM NaCl, 75 mM SDS, 0.5 mM 13C,15N-LABELED TSP9, 90% H2O, 10% D2O
Solvent system: 90% H2O/10% D2O
Sample conditionsIonic strength: 175 mM / pH: 7 / Pressure: 1 atm / Temperature: 298 K

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometerType: Varian INOVA / Manufacturer: Varian / Model: INOVA / Field strength: 600 MHz

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Processing

NMR software
NameVersionDeveloperClassification
CYANA2.1GUENTERTrefinement
VNMR1.1structure solution
Sparky3.72structure solution
NMRPipe97.027.12.56structure solution
CYANA2.1structure solution
RefinementMethod: torsion angle dynamics,simulated annealing / Software ordinal: 1
Details: STRUCTURES ARE BASED ON A TOTAL OF 767 NOE RESTRAINTS (355 INTRA, 278 SEQUENTIAL, 134 MEDIUM and 0 LONG RANGE INTERMOLECULR) AND 38 PHI AND PSI DIHEDRAL ANGLE CONSTRAINTS.
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 100 / Conformers submitted total number: 20

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