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Open data
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Basic information
Entry | Database: PDB / ID: 1byp | ||||||
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Title | E43K,D44K DOUBLE MUTANT PLASTOCYANIN FROM SILENE | ||||||
![]() | PROTEIN (PLASTOCYANIN) | ||||||
![]() | ELECTRON TRANSPORT / ELECTRON TRANSFER / PHOTOSYNTHESIS / ACIDIC PATCH / DOUBLE MUTANT | ||||||
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 | ![]() ![]() | ||||||
![]() | Sugawara, H. / Inoue, T. / Li, C. / Gotowda, M. / Hibino, T. / Takabe, T. / Kai, Y. | ||||||
![]() | ![]() 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: ![]() 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: ![]() Title: Accuracy and Precision in Protein Structure Analysis: Restrained Least-Squares Refinement of the Structure of Poplar Plastocyanin at 1.33 A Resolution Authors: Guss, J.M. / Bartunik, H.D. / Freeman, H.C. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 32.1 KB | Display | ![]() |
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PDB format | ![]() | 21.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 431.9 KB | Display | ![]() |
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Full document | ![]() | 433.8 KB | Display | |
Data in XML | ![]() | 7.3 KB | Display | |
Data in CIF | ![]() | 9.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1byoC ![]() 1pcy C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 10415.667 Da / Num. of mol.: 1 / Mutation: E43K, D44K Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Species: Silene latifolia / Strain: subsp. alba / Organelle: CHLOROPLAST / Production host: ![]() ![]() |
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#2: Chemical | ChemComp-CU / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.54 Å3/Da / Density % sol: 52 % | ||||||||||||||||||||
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Crystal grow | pH: 7 Details: 2.8M AMMONIUM SULFATE, 100MM POTASSIUM PHOSPHATE, pH 7.0 | ||||||||||||||||||||
Crystal grow | *PLUS Method: vapor diffusion, hanging drop | ||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 300 K |
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Diffraction source | Source: ![]() |
Detector | Type: RIGAKU / Detector: IMAGE PLATE / Date: Jan 15, 1995 |
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: 1.75→30 Å / Num. obs: 10737 / % possible obs: 93.6 % / Observed criterion σ(I): 0 / Redundancy: 4.9 % / Rmerge(I) obs: 0.056 |
Reflection | *PLUS Num. measured all: 52627 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1PCY ![]() 1pcy Resolution: 1.75→20 Å / Cross valid method: THROUGHOUT / σ(F): 0
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Refinement step | Cycle: LAST / Resolution: 1.75→20 Å
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Refine LS restraints |
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Software | *PLUS Name: REFMAC / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Lowest resolution: 20 Å / σ(F): 0 / % reflection Rfree: 5 % / Rfactor obs: 0.18 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS |