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Open data
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Basic information
Entry | Database: PDB / ID: 1ylb | ||||||
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Title | NMR solution structure of the reduced spinach plastocyanin | ||||||
![]() | Plastocyanin, chloroplast | ||||||
![]() | ELECTRON TRANSPORT / plastocyanin / copper(+)-containing / electron-transfer / spinach / photosynthesis / blue-copper protein | ||||||
Function / homology | ![]() electron transporter, transferring electrons from cytochrome b6/f complex of photosystem II activity / chloroplast thylakoid lumen / chloroplast thylakoid membrane / copper ion binding Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | SOLUTION NMR / torsion angle dynamics + restrained energy minimization + restrained molecular dynamics | ||||||
![]() | Musiani, F. / Dikiy, A. / Semenov, A.Y. / Ciurli, S. | ||||||
![]() | ![]() Title: Structure of the Intermolecular Complex between Plastocyanin and Cytochrome f from Spinach. Authors: Musiani, F. / Dikiy, A. / Semenov, A.Y. / Ciurli, S. #1: ![]() Title: Crystal Structure of Spinach Plastocyanin at 1.7A Resolution Authors: Xue, Y. / Okvist, M. / Hansson, O. / Young, S. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 41.8 KB | Display | ![]() |
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PDB format | ![]() | 29.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 297.3 KB | Display | ![]() |
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Full document | ![]() | 297 KB | Display | |
Data in XML | ![]() | 3.4 KB | Display | |
Data in CIF | ![]() | 4.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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NMR ensembles |
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Components
#1: Protein | Mass: 10420.557 Da / Num. of mol.: 1 / Fragment: Reduced spinach plastocyanin (Residues 70-168) / Source method: isolated from a natural source / Source: (natural) ![]() |
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#2: Chemical | ChemComp-CU1 / |
-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR | ||||||||||||
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NMR experiment |
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Sample preparation
Details | Contents: 1-2 mM wild type reduced spinach plastocyanin, 50mM sodium phosphate buffer Solvent system: 90% H2O/10% D2O |
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Sample conditions | Ionic strength: 50 mM sodium phosphate / pH: 7.5 / Pressure: ambient / Temperature: 293 K |
-NMR measurement
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M | |||||||||||||||
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Radiation wavelength | Relative weight: 1 | |||||||||||||||
NMR spectrometer |
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Processing
NMR software |
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Refinement | Method: torsion angle dynamics + restrained energy minimization + restrained molecular dynamics Software ordinal: 1 Details: The structure was calculated using dipolar (NOESY) derived constraints supplemented with phi and psi dihedral angle constraints as well as with hydrogen bond constraints. The mean structure ...Details: The structure was calculated using dipolar (NOESY) derived constraints supplemented with phi and psi dihedral angle constraints as well as with hydrogen bond constraints. The mean structure of the DYANA family was initially subjected to restrained energy minimization in vacuo and subsequently to restrained molecular dynamics in explicit water medium. For further experimental details please refer to the publication. | ||||||||||||||||||||
NMR representative | Selection criteria: the structure was obtained subjecting the mean structure of the dyana family to the restrained energy minimization and subsequent restrained molecular dynamics | ||||||||||||||||||||
NMR ensemble | Conformers submitted total number: 1 |