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Open data
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Basic information
Entry | Database: PDB / ID: 6j88 | ||||||
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Title | Crystal structure of HinD with benzo[b]thiophen analog | ||||||
![]() | Nocardicin N-oxygenase | ||||||
![]() | OXIDOREDUCTASE / P450 / indolactam / oxidation | ||||||
Function / homology | ![]() cholest-4-en-3-one 26-monooxygenase activity / steroid hydroxylase activity / cholesterol catabolic process / iron ion binding / heme binding Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Fei, H. / Mori, T. / Abe, I. | ||||||
![]() | ![]() Title: Molecular basis for the P450-catalyzed C-N bond formation in indolactam biosynthesis. Authors: He, F. / Mori, T. / Morita, I. / Nakamura, H. / Alblova, M. / Hoshino, S. / Awakawa, T. / Abe, I. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 172 KB | Display | ![]() |
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PDB format | ![]() | 132.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.7 MB | Display | ![]() |
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Full document | ![]() | 1.7 MB | Display | |
Data in XML | ![]() | 33 KB | Display | |
Data in CIF | ![]() | 45.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6j82SC ![]() 6j83C ![]() 6j84C ![]() 6j85C ![]() 6j86C ![]() 6j87C 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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1 | ![]()
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2 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 47925.695 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Gene: SAMN05444320_102263 / Production host: ![]() ![]() #2: Chemical | #3: Chemical | #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 1.93 Å3/Da / Density % sol: 36.18 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop Details: 100 mM MES (pH 6.5) containing 1200 mM (NH4)2HPO4 and 100 mM NaCl |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS EIGER X 4M / Detector: PIXEL / Date: Jun 26, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.1 Å / Relative weight: 1 |
Reflection | Resolution: 2.35→47.631 Å / Num. obs: 29547 / % possible obs: 98.1 % / Redundancy: 3 % / CC1/2: 0.947 / Rmerge(I) obs: 0.182 / Net I/σ(I): 3.1 |
Reflection shell | Resolution: 2.35→2.43 Å / Redundancy: 3 % / Rmerge(I) obs: 0.536 / Mean I/σ(I) obs: 1.6 / Num. unique obs: 2923 / CC1/2: 0.456 / % possible all: 98.1 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 6J82 Resolution: 2.35→47.631 Å / Cross valid method: FREE R-VALUE / σ(F): 1.42 / Phase error: 24.48
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.35→47.631 Å
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Refine LS restraints |
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LS refinement shell |
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