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Open data
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Basic information
Entry | Database: PDB / ID: 7y9o | ||||||
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Title | Crystal structure of a CYP109B4 variant from Bacillus sonorensis | ||||||
![]() | 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 | ![]()
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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 | ![]() | 109.8 KB | Display | ![]() |
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PDB format | ![]() | 78.9 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 ![]() 7y98C ![]() 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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1 |
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Unit cell |
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Components
#1: Protein | Mass: 46508.797 Da / Num. of mol.: 1 Mutation: C40Y/N49S/L264F/L240V/S387F/V84L/V292S/I291T/M290F/F294I Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() | ||||
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#2: Chemical | ChemComp-HEM / ![]() | ||||
#3: Chemical | ChemComp-IMD / ![]() | ||||
#4: Chemical | #5: Water | ChemComp-HOH / | ![]() Has ligand of interest | Y | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.26 Å3/Da / Density % sol: 45.66 % |
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Crystal grow![]() | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7 Details: 0.2M calcium acetate hydrate, 0.1M Tris (pH 7.0), 18% Polyethylene glycol 3000 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: LIQUID ANODE / Type: BRUKER METALJET / Wavelength: 1.34138 Å |
Detector | Type: Bruker PHOTON III / Detector: PIXEL / Date: Dec 15, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 1.84→38.06 Å / Num. obs: 37491 / % possible obs: 99.8 % / Redundancy: 8.04 % / Rmerge(I) obs: 0.0769 / Net I/σ(I): 15.9 |
Reflection shell | Resolution: 1.84→1.87 Å / Redundancy: 3.69 % / Rmerge(I) obs: 0.3271 / Num. unique obs: 1732 / % possible all: 100 |
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Processing
Software |
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Refinement | Method to determine structure![]() ![]() Starting model: 4RM4 Resolution: 1.84→38.06 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.937 / SU B: 3.313 / SU ML: 0.098 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.151 / ESU R Free: 0.135 / 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: 93.95 Å2 / Biso mean: 25.917 Å2 / Biso min: 11.98 Å2
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Refinement step | Cycle: final / Resolution: 1.84→38.06 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.84→1.888 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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