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- PDB-5yo5: Crystal Structure of B562RIL with engineered disulfide bond A20C-Q25C -
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Open data
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Basic information
Entry | Database: PDB / ID: 5yo5 | ||||||
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Title | Crystal Structure of B562RIL with engineered disulfide bond A20C-Q25C | ||||||
![]() | Soluble cytochrome b562 | ||||||
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Function / homology | Cytochrome b562 / Cytochrome b562 / Cytochrome c/b562 / ![]() ![]() ![]() ![]() ![]() | ||||||
Biological species | ![]() ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Pu, M. / Xu, Z. / Song, G. / Liu, Z.J. | ||||||
![]() | ![]() Title: Protein crystal quality oriented disulfide bond engineering. Authors: Pu, M. / Xu, Z. / Peng, Y. / Hou, Y. / Liu, D. / Wang, Y. / Liu, H. / Song, G. / Liu, Z.J. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 180.9 KB | Display | ![]() |
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PDB format | ![]() | 146.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 5ym7C ![]() 5yo3C ![]() 5yo4C ![]() 5yo6C ![]() 5yobC ![]() 5yocC ![]() 5yoeC ![]() 5yogC ![]() 1m6tS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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8 | ![]()
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Unit cell |
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Components on special symmetry positions |
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Components
#1: Protein | Mass: 11863.386 Da / Num. of mol.: 8 / Mutation: M7W, H102I, R106L, A20C, Q25C Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() ![]() #2: Water | ChemComp-HOH / | ![]() |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.16 Å3/Da / Density % sol: 43.2 % |
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Crystal grow![]() | Temperature: 292 K / Method: vapor diffusion, hanging drop Details: 3.2M NH4(SO4), 0.1M Bicine 2.44mM N-octanoylsucrose PH range: 9.0-9.4 |
-Data collection
Diffraction | Mean temperature: 100 K / Ambient temp details: Liquid nitrogen |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MAR CCD 130 mm / Detector: CCD / Date: Aug 18, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 2.2→37.7 Å / Num. obs: 79301 / % possible obs: 99 % / Redundancy: 3.7 % / Biso Wilson estimate: 30.41 Å2 / Net I/σ(I): 12.35 |
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Processing
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Refinement | Method to determine structure![]() ![]() Starting model: 1M6T Resolution: 2.2→37.7 Å / SU ML: 0.29 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 28.94
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.2→37.7 Å
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Refine LS restraints |
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LS refinement shell |
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