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Yorodumi- PDB-4h4u: Crystal Structure of Ferredoxin reductase, BphA4 T176R mutant (re... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4h4u | ||||||
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Title | Crystal Structure of Ferredoxin reductase, BphA4 T176R mutant (reduced form) | ||||||
Components | Biphenyl dioxygenase ferredoxin reductase subunit | ||||||
Keywords | OXIDOREDUCTASE / Flavoprotein | ||||||
Function / homology | Function and homology information oxidoreductase activity, acting on NAD(P)H / dioxygenase activity / flavin adenine dinucleotide binding / cytoplasm Similarity search - Function | ||||||
Biological species | Acidovorax (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å | ||||||
Authors | Nishizawa, A. / Harada, A. / Senda, M. / Tachihara, Y. / Muramatsu, D. / Kishigami, S. / Mori, S. / Sugiyama, K. / Senda, T. / Kimura, S. | ||||||
Citation | Journal: To be Published 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4h4u.cif.gz | 97.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4h4u.ent.gz | 71.9 KB | Display | PDB format |
PDBx/mmJSON format | 4h4u.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4h4u_validation.pdf.gz | 1 MB | Display | wwPDB validaton report |
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Full document | 4h4u_full_validation.pdf.gz | 1 MB | Display | |
Data in XML | 4h4u_validation.xml.gz | 19.3 KB | Display | |
Data in CIF | 4h4u_validation.cif.gz | 27.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/h4/4h4u ftp://data.pdbj.org/pub/pdb/validation_reports/h4/4h4u | HTTPS FTP |
-Related structure data
Related structure data | 4h4pC 4h4qC 4h4rC 4h4sC 4h4tC 4h4vC 4h4wC 4h4xC 4h4yC 4h4zC 4h50C 2yvfS 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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Unit cell |
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-Components
#1: Protein | Mass: 43277.273 Da / Num. of mol.: 1 / Mutation: T176R Source method: isolated from a genetically manipulated source Source: (gene. exp.) Acidovorax (bacteria) / Strain: KKS102 / Gene: bphA4 / Production host: Escherichia coli (E. coli) / References: UniProt: E7FJB9, ferredoxin-NAD+ reductase | ||
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#2: Chemical | ChemComp-NDP / | ||
#3: Chemical | ChemComp-FAD / | ||
#4: Chemical | ChemComp-FMT / #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.75 Å3/Da / Density % sol: 55.21 % |
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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: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NE3A / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 270 / Detector: CCD / Date: Oct 15, 2011 |
Radiation | Monochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.6→84.9 Å / Num. all: 62024 / Num. obs: 62024 / % possible obs: 95.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 18.34 Å2 |
Reflection shell | Resolution: 1.6→1.69 Å / % possible all: 99.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2YVF Resolution: 1.6→42.545 Å / Occupancy max: 1 / Occupancy min: 0 / FOM work R set: 0.8418 / SU ML: 0.18 / σ(F): 1.99 / Phase error: 22.35 / 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: 70.85 Å2 / Biso mean: 22.6126 Å2 / Biso min: 7.71 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.6→42.545 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: 22
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