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Open data
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Basic information
Entry | Database: PDB / ID: 7buh | ||||||
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Title | Reduced ferredoxin of carbazole 1,9a-dioxygenase | ||||||
![]() | Ferredoxin CarAc | ||||||
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Function / homology | ![]() carbazole catabolic process / ![]() ![]() ![]() Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Matsuzawa, J. / Wang, Y.X. / Suzuki-Minakuchi, C. / Nojiri, H. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Reduced ferredoxin of carbazole 1,9a-dioxygenase Authors: Matsuzawa, J. / Wang, Y.X. / Suzuki-Minakuchi, C. / Nojiri, H. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 40.9 KB | Display | ![]() |
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PDB format | ![]() | 25.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 1vckS 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 on special symmetry positions |
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Components
#1: Protein | Mass: 12448.059 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() |
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#2: Chemical | ChemComp-FES / ![]() |
#3: Chemical | ChemComp-NA / |
#4: Chemical | ChemComp-EDO / ![]() |
#5: Water | ChemComp-HOH / ![]() |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 1.89 Å3/Da / Density % sol: 34.81 % |
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Crystal grow![]() | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: Buffer: 5 mM Tris pH 7.5, Reservior: 0.2 M Ammonium acetate, 0.1 M Sodium acetate trihydrate pH 4.1, 30% w/v Polyethylene glycol 4000 |
-Data collection
Diffraction | Mean temperature: 90 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: RAYONIX MX225HE / Detector: CCD / Date: Jul 20, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 1.79→45.45 Å / Num. obs: 9143 / % possible obs: 99.9 % / Redundancy: 26.2 % / Rmerge(I) obs: 0.15 / Net I/σ(I): 29.6 |
Reflection shell | Resolution: 1.79→1.83 Å / Rmerge(I) obs: 0.829 / Num. unique obs: 532 |
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Processing
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Refinement | Method to determine structure![]() ![]() Starting model: 1VCK Resolution: 1.79→45.34 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.954 / SU B: 2.704 / SU ML: 0.083 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.13 / ESU R Free: 0.123 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 94.23 Å2 / Biso mean: 19.798 Å2 / Biso min: 9.48 Å2
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Refinement step | Cycle: final / Resolution: 1.79→45.34 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.794→1.84 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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