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- PDB-5yob: Crystal Structure of flavodoxin without engineered disulfide bond -
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Open data
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Basic information
Entry | Database: PDB / ID: 5yob | ||||||
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Title | Crystal Structure of flavodoxin without engineered disulfide bond | ||||||
![]() | Flavodoxin | ||||||
![]() | ELECTRON TRANSPORT / fusion partner / FMN-binding protein / oxidation | ||||||
Function / homology | ![]() | ||||||
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 | ![]() | 52 KB | Display | ![]() |
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PDB format | ![]() | 34.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 773.9 KB | Display | ![]() |
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Full document | ![]() | 774.9 KB | Display | |
Data in XML | ![]() | 11.4 KB | Display | |
Data in CIF | ![]() | 16.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5ym7C ![]() 5yo3C ![]() 5yo4C ![]() 5yo5C ![]() 5yo6C ![]() 5yocC ![]() 5yoeC ![]() 5yogC ![]() 1j8qS 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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Unit cell |
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Components
#1: Protein | Mass: 15788.223 Da / Num. of mol.: 1 / Mutation: Y98W Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Strain: Hildenborough / ATCC 29579 / DSM 644 / NCIMB 8303 / Gene: DVU_2680 / Production host: ![]() ![]() | ||
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#2: Chemical | ChemComp-FMN / | ||
#3: Chemical | #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.32 Å3/Da / Density % sol: 46.87 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / Details: Tris-HCL 0.1M Ammonium Sulfate 3.2M / PH range: 7.0-7.5 |
-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: Jul 6, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9793 Å / Relative weight: 1 |
Reflection | Resolution: 1.142→31.656 Å / Num. obs: 38709 / % possible obs: 75 % / Redundancy: 4.4 % / Net I/σ(I): 32.21 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1J8Q Resolution: 1.142→31.656 Å / SU ML: 0.1 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 24.07 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.142→31.656 Å
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Refine LS restraints |
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LS refinement shell |
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