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Yorodumi- PDB-1j5c: SOLUTION STRUCTURE OF OXIDIZED PARAMAGNETIC CU(II) PLASTOCYANIN F... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1j5c | |||||||||
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Title | SOLUTION STRUCTURE OF OXIDIZED PARAMAGNETIC CU(II) PLASTOCYANIN FROM SYNECHOCYSTIS PCC6803 | |||||||||
Components | PLASTOCYANIN | |||||||||
Keywords | ELECTRON TRANSPORT / copper protein beta barrel electron transfer | |||||||||
Function / homology | Function and homology information plasma membrane-derived thylakoid membrane / electron transfer activity / copper ion binding Similarity search - Function | |||||||||
Biological species | Synechocystis sp. PCC 6803 (bacteria) | |||||||||
Method | SOLUTION NMR / torsion angle dynamics | |||||||||
Authors | Bertini, I. / Ciurli, S. / Dikiy, A. / Fernandez, C.O. / Luchinat, C. / Safarov, N. / Shumilin, S. / Vila, A.J. | |||||||||
Citation | Journal: J.Am.Chem.Soc. / Year: 2001 Title: The first solution structure of a paramagnetic copper(II) protein: the case of oxidized plastocyanin from the cyanobacterium Synechocystis PCC6803. Authors: Bertini, I. / Ciurli, S. / Dikiy, A. / Fernandez, C.O. / Luchinat, C. / Safarov, N. / Shumilin, S. / Vila, A.J. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1j5c.cif.gz | 956.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1j5c.ent.gz | 801.9 KB | Display | PDB format |
PDBx/mmJSON format | 1j5c.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1j5c_validation.pdf.gz | 342.2 KB | Display | wwPDB validaton report |
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Full document | 1j5c_full_validation.pdf.gz | 624.1 KB | Display | |
Data in XML | 1j5c_validation.xml.gz | 68.8 KB | Display | |
Data in CIF | 1j5c_validation.cif.gz | 106.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/j5/1j5c ftp://data.pdbj.org/pub/pdb/validation_reports/j5/1j5c | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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NMR ensembles |
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-Components
#1: Protein | Mass: 10249.430 Da / Num. of mol.: 1 / Mutation: D98E Source method: isolated from a genetically manipulated source Source: (gene. exp.) Synechocystis sp. PCC 6803 (bacteria) / Strain: PCC6803 / Plasmid: PET3D / Production host: Escherichia coli (E. coli) / Strain (production host): BLR(DE3) / References: UniProt: P21697 |
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#2: Chemical | ChemComp-CU / |
-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR | ||||||||||||||||||||
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NMR experiment |
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-Sample preparation
Details | Contents: 3 mM plastocyanin U-15N 50 mM phosphate buffer / Solvent system: 90% H2O/10% D2O |
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Sample conditions | Ionic strength: 50 mM phosphate / pH: 5.2 / Pressure: ambient / Temperature: 295 K |
Crystal grow | *PLUS Method: other / Details: NMR |
-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 / Software ordinal: 1 Details: The protein contains paramagnetic copper(II), whose electronic relaxation times are quite unfavorable for NMR solution studies. The structure has been solved on the basis of 1041 meaningful ...Details: The protein contains paramagnetic copper(II), whose electronic relaxation times are quite unfavorable for NMR solution studies. The structure has been solved on the basis of 1041 meaningful NOESY cross peaks, 18 1D NOEs, 26 T1 values, 96 dihedral angle constraints and 18 H-bonds. The detection of broad hyperfine shifted signals and their full assignment allowed the identification of the copper(II) ligands and the determination of the Cu-S-C-H dihedral angle for the coordinated cysteine. The global root mean square deviation from the mean structure for the solution structure family is 0.72 and 1.16 for backbone and heavy atoms, respectively. | ||||||||||||||||||||
NMR representative | Selection criteria: fewest violations | ||||||||||||||||||||
NMR ensemble | Conformer selection criteria: target function / Conformers calculated total number: 400 / Conformers submitted total number: 35 |