+Open data
-Basic information
Entry | Database: PDB / ID: 1byo | ||||||
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Title | WILD-TYPE PLASTOCYANIN FROM SILENE | ||||||
Components | PROTEIN (PLASTOCYANIN) | ||||||
Keywords | ELECTRON TRANSPORT / ELECTRON TRANSFER / PHOTOSYNTHESIS | ||||||
Function / homology | Function and homology information chloroplast thylakoid membrane / electron transfer activity / copper ion binding Similarity search - Function | ||||||
Biological species | Silene latifolia subsp. alba (white campion) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2 Å | ||||||
Authors | Sugawara, H. / Inoue, T. / Li, C. / Gotowda, M. / Hibino, T. / Takabe, T. / Kai, Y. | ||||||
Citation | Journal: J.Biochem.(Tokyo) / Year: 1999 Title: Crystal structures of wild-type and mutant plastocyanins from a higher plant, Silene. Authors: Sugawara, H. / Inoue, T. / Li, C. / Gotowda, M. / Hibino, T. / Takabe, T. / Kai, Y. #1: Journal: Acta Crystallogr.,Sect.D / Year: 1997 Title: Crystallization and Preliminary X-Ray Studies of Plastocyanin from Silene Expressed in E. Coli Authors: Li, C. / Inoue, T. / Gotowda, M. / Hamada, K. / Nishio, N. / Hibino, T. / Takabe, T. / Kai, Y. #2: Journal: Acta Crystallogr., Sect.B / Year: 1992 Title: Accuracy and Precision in Protein Structure Analysis: Restrained Least-Squares Refinement of the Structure of Poplar Plastocyanin at 1.33 Angstroms Resolution Authors: Guss, J.M. / Bartunik, H.D. / Freeman, H.C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1byo.cif.gz | 49.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1byo.ent.gz | 35.9 KB | Display | PDB format |
PDBx/mmJSON format | 1byo.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/by/1byo ftp://data.pdbj.org/pub/pdb/validation_reports/by/1byo | HTTPS FTP |
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-Related structure data
Related structure data | 1bypC 1pcy C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 10401.509 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Silene latifolia subsp. alba (white campion) Species: Silene latifolia / Strain: subsp. alba / Organelle: CHLOROPLAST / Production host: Escherichia coli (E. coli) / References: UniProt: P07030 #2: Chemical | #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.64 Å3/Da / Density % sol: 53 % | ||||||||||||||||||||
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Crystal grow | pH: 5.5 Details: 53% SATURATED AMMONIUM SULFATE, 0.1 M SODIUM ACETATE BUFFER, pH 5.5 | ||||||||||||||||||||
Crystal grow | *PLUS pH: 7 / Method: vapor diffusion, hanging drop | ||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 285 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.5418 |
Detector | Type: RIGAKU / Detector: IMAGE PLATE / Date: Dec 15, 1994 |
Radiation | Monochromator: NI FILTER / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2→30 Å / Num. obs: 11515 / % possible obs: 94.2 % / Observed criterion σ(I): 0 / Redundancy: 3.8 % / Rmerge(I) obs: 0.06 |
Reflection | *PLUS Num. measured all: 44196 / Rmerge(I) obs: 0.06 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1PCY 1pcy Resolution: 2→20 Å / Cross valid method: THROUGHOUT / σ(F): 0
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Refinement step | Cycle: LAST / Resolution: 2→20 Å
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Refine LS restraints |
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Software | *PLUS Name: REFMAC / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Highest resolution: 2 Å / Lowest resolution: 20 Å / σ(F): 0 / % reflection Rfree: 5 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS Type: p_planar_d / Dev ideal target: 0.05 |