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- PDB-4h4x: Crystal Structure of Ferredoxin reductase, BphA4 E175A/T176R/Q177... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4h4x | ||||||
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Title | Crystal Structure of Ferredoxin reductase, BphA4 E175A/T176R/Q177G mutant (oxidized form) | ||||||
![]() | Biphenyl dioxygenase ferredoxin reductase subunit | ||||||
![]() | OXIDOREDUCTASE / Flavoprotein | ||||||
Function / homology | ![]() oxidoreductase activity, acting on NAD(P)H / dioxygenase activity / flavin adenine dinucleotide binding / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Nishizawa, A. / Harada, A. / Senda, M. / Tachihara, Y. / Muramatsu, D. / Kishigami, S. / Mori, S. / Sugiyama, K. / Senda, T. / Kimura, S. | ||||||
![]() | ![]() Title: Random Mutagenesis with the Project Assessment for Complete Conversion of Co-Factor Specificity of a Ferredoxin Reductase BphA4 Authors: Nishizawa, A. / Harada, A. / Senda, M. / Tachihara, Y. / Muramatsu, D. / Kishigami, S. / Mori, S. / Sugiyama, K. / Senda, T. / Kimura, S. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 98.6 KB | Display | ![]() |
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PDB format | ![]() | 72.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 707.3 KB | Display | ![]() |
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Full document | ![]() | 711.4 KB | Display | |
Data in XML | ![]() | 19.5 KB | Display | |
Data in CIF | ![]() | 29.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4h4pC ![]() 4h4qC ![]() 4h4rC ![]() 4h4sC ![]() 4h4tC ![]() 4h4uC ![]() 4h4vC ![]() 4h4wC ![]() 4h4yC ![]() 4h4zC ![]() 4h50C ![]() 2gqwS 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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1 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 43148.164 Da / Num. of mol.: 1 / Mutation: E175A, T176R, Q177G Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() | ||
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#2: Chemical | ChemComp-FAD / | ||
#3: Chemical | ChemComp-GOL / | ||
#4: Chemical | ChemComp-FMT / #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.76 Å3/Da / Density % sol: 55.37 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.2 Details: 2.5M Sodium formate, 0.1M acetate buffer, pH 5.2, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 95 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: RAYONIX MX-300 / Detector: CCD / Date: Aug 4, 2012 |
Radiation | Monochromator: S1 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97948 Å / Relative weight: 1 |
Reflection | Resolution: 1.5→19.58 Å / Num. all: 76902 / Num. obs: 76902 / % possible obs: 98.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 15.33 Å2 |
Reflection shell | Resolution: 1.5→1.58 Å / % possible all: 97.1 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 2GQW Resolution: 1.5→19.58 Å / Occupancy max: 1 / Occupancy min: 0.09 / FOM work R set: 0.8718 / SU ML: 0.12 / σ(F): 1.99 / Phase error: 19.53 / 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 51.9 Å2 / Biso mean: 18.9694 Å2 / Biso min: 7.75 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.5→19.58 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 27
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