+Open data
-Basic information
Entry | Database: PDB / ID: 2bzc | ||||||
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Title | Oxidized and reduced structures of a mutant Plastocyanin of fern | ||||||
Components | PLASTOCYANIN | ||||||
Keywords | ELECTRON TRANSPORT / PLASTOCYANIN / FERN / CHLOROPLAST / MEMBRANE / METAL-BINDING | ||||||
Function / homology | Function and homology information 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 | DRYOPTERIS CRASSIRHIZOMA (plant) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.79 Å | ||||||
Authors | Hulsker, R. / Thomassen, E.A.J. / Ubbink, M. | ||||||
Citation | Journal: J.Am.Chem.Soc. / Year: 2007 Title: Protonation of a Histidine Copper Ligand in Fern Plastocyanin. Authors: Hulsker, R. / Mery, A. / Thomassen, E.A.J. / Ranieri, A. / Sola, M. / Verbeet, M.P. / Kohzuma, T. / Ubbink, M. #1: Journal: Biochemistry / Year: 1999 Title: Structure Comparison between Oxidezed and Reduced Plastocyanin from a Fer, Dryopteris Crassirhizoma Authors: Inoue, T. / Gotowda, M. / Sugawara, H. / Kohzuma, T. / Yoshizaki, F. / Sugimura, Y. / Kai, Y. | ||||||
History |
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Remark 650 | HELIX DETERMINATION METHOD: AUTHOR PROVIDED. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2bzc.cif.gz | 33.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2bzc.ent.gz | 22.6 KB | Display | PDB format |
PDBx/mmJSON format | 2bzc.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2bzc_validation.pdf.gz | 425.4 KB | Display | wwPDB validaton report |
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Full document | 2bzc_full_validation.pdf.gz | 426 KB | Display | |
Data in XML | 2bzc_validation.xml.gz | 6.9 KB | Display | |
Data in CIF | 2bzc_validation.cif.gz | 8.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bz/2bzc ftp://data.pdbj.org/pub/pdb/validation_reports/bz/2bzc | HTTPS FTP |
-Related structure data
Related structure data | 2bz7C 1kdiS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 10826.036 Da / Num. of mol.: 1 / Mutation: YES Source method: isolated from a genetically manipulated source Details: REDUCED FORM THE REDUCED FORM WAS OBTAINED BY REDUCING THE OXIDIZED CRYSTAL FOR 10 MINUTES IN CRYSTALLISATION BUFFER INCLUDING 0.01M SODIUM ASCORBATE Source: (gene. exp.) DRYOPTERIS CRASSIRHIZOMA (plant) / Plasmid: PETG36P / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q7SIB8 |
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#2: Chemical | ChemComp-CU1 / |
#3: Water | ChemComp-HOH / |
Compound details | ENGINEERED RESIDUE IN CHAIN A, GLY 36 TO PRO PARTICIPATES IN ELECTRON TRANSFER BETWEEN CYTOCHROME ...ENGINEERED |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.1 Å3/Da / Density % sol: 40.6 % |
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Crystal grow | pH: 4.5 Details: 2.6 M AMMONIUM SULPHATE, 0.1M SODIUM ACETATE PH 4.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.95372 |
Detector | Type: MARRESEARCH / Detector: CCD / Date: May 6, 2005 / Details: MIRRORS |
Radiation | Monochromator: SI (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.95372 Å / Relative weight: 1 |
Reflection | Resolution: 1.79→23.9 Å / Num. obs: 8720 / % possible obs: 100 % / Redundancy: 21.45 % / Biso Wilson estimate: 20.4 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 7.43 |
Reflection shell | Resolution: 1.79→1.89 Å / Redundancy: 21.22 % / Rmerge(I) obs: 0.23 / Mean I/σ(I) obs: 3.25 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1KDI Resolution: 1.79→30 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.914 / SU B: 6.289 / SU ML: 0.109 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.142 / ESU R Free: 0.145 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 30.04 Å2
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Refinement step | Cycle: LAST / Resolution: 1.79→30 Å
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Refine LS restraints |
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