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Yorodumi- PDB-4h50: Crystal Structure of Ferredoxin reductase, BphA4 E175Q/T1776R/Q17... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4h50 | ||||||
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Title | Crystal Structure of Ferredoxin reductase, BphA4 E175Q/T1776R/Q177G 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: 2.65 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 | 4h50.cif.gz | 91.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4h50.ent.gz | 66.4 KB | Display | PDB format |
PDBx/mmJSON format | 4h50.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4h50_validation.pdf.gz | 1007.4 KB | Display | wwPDB validaton report |
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Full document | 4h50_full_validation.pdf.gz | 1012 KB | Display | |
Data in XML | 4h50_validation.xml.gz | 17 KB | Display | |
Data in CIF | 4h50_validation.cif.gz | 22.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/h5/4h50 ftp://data.pdbj.org/pub/pdb/validation_reports/h5/4h50 | HTTPS FTP |
-Related structure data
Related structure data | 4h4pC 4h4qC 4h4rC 4h4sC 4h4tC 4h4uC 4h4vC 4h4wC 4h4xC 4h4yC 4h4zC 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
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 43205.211 Da / Num. of mol.: 1 / Mutation: E175Q, T176R, Q177G 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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-Non-polymers , 5 types, 51 molecules
#2: Chemical | ChemComp-FAD / | ||||
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#3: Chemical | ChemComp-NAP / | ||||
#4: Chemical | ChemComp-FMT / #5: Chemical | ChemComp-GOL / | #6: 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: 55.32 % |
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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: APS / Beamline: 23-ID-B / Wavelength: 0.97948 Å |
Detector | Type: RAYONIX MX-300 / Detector: CCD / Date: Aug 4, 2012 |
Radiation | Monochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97948 Å / Relative weight: 1 |
Reflection | Resolution: 2.65→19.645 Å / Num. all: 14744 / Num. obs: 14744 / % possible obs: 99.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 43.93 Å2 |
Reflection shell | Resolution: 2.65→2.79 Å / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2YVF Resolution: 2.65→19.645 Å / Occupancy max: 1 / Occupancy min: 0.38 / FOM work R set: 0.8179 / SU ML: 0.35 / σ(F): 2 / Phase error: 23.81 / 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: 71.25 Å2 / Biso mean: 29.2354 Å2 / Biso min: 6.02 Å2 | ||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.65→19.645 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: 5 / % reflection obs: 100 %
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