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- PDB-1ylb: NMR solution structure of the reduced spinach plastocyanin -

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Basic information

Entry
Database: PDB / ID: 1ylb
TitleNMR solution structure of the reduced spinach plastocyanin
ComponentsPlastocyanin, chloroplast
KeywordsELECTRON TRANSPORT / plastocyanin / copper(+)-containing / electron-transfer / spinach / photosynthesis / blue-copper protein
Function / homology
Function and homology information


: / chloroplast thylakoid lumen / chloroplast thylakoid membrane / copper ion binding
Similarity search - Function
Plastocyanin / Blue (type 1) copper protein, plastocyanin-type / Blue (type 1) copper domain / Copper binding proteins, plastocyanin/azurin family / Blue (type 1) copper protein, binding site / Type-1 copper (blue) proteins signature. / Cupredoxins - blue copper proteins / Cupredoxin / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
COPPER (I) ION / Plastocyanin, chloroplastic
Similarity search - Component
Biological speciesSpinacia oleracea (spinach)
MethodSOLUTION NMR / torsion angle dynamics + restrained energy minimization + restrained molecular dynamics
AuthorsMusiani, F. / Dikiy, A. / Semenov, A.Y. / Ciurli, S.
Citation
Journal: J.Biol.Chem. / Year: 2005
Title: Structure of the Intermolecular Complex between Plastocyanin and Cytochrome f from Spinach.
Authors: Musiani, F. / Dikiy, A. / Semenov, A.Y. / Ciurli, S.
#1: Journal: Protein Sci. / Year: 1998
Title: Crystal Structure of Spinach Plastocyanin at 1.7A Resolution
Authors: Xue, Y. / Okvist, M. / Hansson, O. / Young, S.
History
DepositionJan 19, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 5, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 2, 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_conn_angle / pdbx_struct_oper_list / struct_conn / struct_site
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 / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4May 22, 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
B: Plastocyanin, chloroplast
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,4842
Polymers10,4211
Non-polymers641
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)1 / -
RepresentativeModel #1the structure was obtained subjecting the mean structure of the dyana family to the restrained energy minimization and subsequent restrained molecular dynamics

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Components

#1: Protein Plastocyanin, chloroplast


Mass: 10420.557 Da / Num. of mol.: 1 / Fragment: Reduced spinach plastocyanin (Residues 70-168) / Source method: isolated from a natural source / Source: (natural) Spinacia oleracea (spinach) / References: UniProt: P00289
#2: Chemical ChemComp-CU1 / COPPER (I) ION


Mass: 63.546 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cu

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D NOESY
1212D TOCSY

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Sample preparation

DetailsContents: 1-2 mM wild type reduced spinach plastocyanin, 50mM sodium phosphate buffer
Solvent system: 90% H2O/10% D2O
Sample conditionsIonic strength: 50 mM sodium phosphate / pH: 7.5 / Pressure: ambient / Temperature: 293 K

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AVANCEBrukerAVANCE8001
Bruker AVANCEBrukerAVANCE5002

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Processing

NMR software
NameVersionDeveloperClassification
XwinNMR1.3Brukercollection
DYANA1.5Guntert, P., Mumenthaler, C., and Wuthrich, K.structure solution
Amber6Case, D. A., Pearlman, D. A., Caldwell, J. W., Cheatham III, T. E., Ross, W. S., Simmerling, C. L., Darden, T. A., Merz, K. M., Stanton, R. V., Cheng, A. L., Vincent, J. J., Crowley, M., Tsui, V., Radmer, R. J., Duan, Y., Pitera, J., Massova, I., Seibel, G. L., Singh, U. C., Weiner, P. K., and Kollman, P. A.refinement
XEASY1.3Bartels, C., Xia, T., Billeter, M., Guntert, P., and Wuthrich, K.data analysis
RefinementMethod: 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 representativeSelection criteria: the structure was obtained subjecting the mean structure of the dyana family to the restrained energy minimization and subsequent restrained molecular dynamics
NMR ensembleConformers submitted total number: 1

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