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- PDB-7y98: Crystal structure of CYP109B4 from Bacillus Sonorensis in complex... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7y98 | ||||||
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Title | Crystal structure of CYP109B4 from Bacillus Sonorensis in complex with Testosterone | ||||||
![]() | Cytochrome P450 monooxygenase YjiB | ||||||
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Function / homology | ![]() ![]() ![]() ![]() Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Shen, P.P. / Huang, J.-W. / Li, X. / Liu, W.D. / Chen, C.-C. / Guo, R.-T. | ||||||
Funding support | 1items
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![]() | ![]() Title: Rationally Controlling Selective Steroid Hydroxylation via Scaffold Sampling of a P450 Family Authors: Zhang, X. / Shen, P. / Zhao, J. / Chen, Y. / Li, X. / Huang, J.W. / Zhang, L. / Li, Q. / Gao, C. / Xing, Q. / Chen, C.C. / Guo, R.T. / Li, A. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 170.5 KB | Display | ![]() |
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PDB format | ![]() | 133.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 7y97C ![]() 7y9oC ![]() 4rm4S S: Starting model for refinement C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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2 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 46490.848 Da / Num. of mol.: 2 / Mutation: C40Y,N49S,L264F Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() #2: Chemical | ![]() #3: Chemical | ![]() #4: Water | ChemComp-HOH / | ![]() Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.86 Å3/Da / Density % sol: 57.06 % / Mosaicity: 1.043 ° |
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Crystal grow![]() | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 5.6 Details: 20% PEG 4000, 0.1M Na-Citrate pH 5.6, 20% iso-Propanol |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: RAYONIX MX-300 / Detector: CCD / Date: Dec 19, 2019 |
Radiation | Monochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 2.27→25 Å / Num. obs: 45487 / % possible obs: 94.1 % / Redundancy: 4.1 % / Rmerge(I) obs: 0.059 / Net I/σ(I): 12.4 |
Reflection shell | Resolution: 2.27→2.35 Å / Redundancy: 4 % / Rmerge(I) obs: 0.725 / Num. unique obs: 4006 / % possible all: 89.7 |
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Processing
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Refinement | Method to determine structure![]() ![]() Starting model: 4RM4 Resolution: 2.27→24.65 Å / SU ML: 0.35 / Cross valid method: THROUGHOUT / σ(F): 1.37 / Phase error: 35.91 / 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: 135.63 Å2 / Biso mean: 56.54 Å2 / Biso min: 28.11 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.27→24.65 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 10
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