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Yorodumi- PDB-7y98: Crystal structure of CYP109B4 from Bacillus Sonorensis in complex... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7y98 | ||||||
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Title | Crystal structure of CYP109B4 from Bacillus Sonorensis in complex with Testosterone | ||||||
Components | Cytochrome P450 monooxygenase YjiB | ||||||
Keywords | OXIDOREDUCTASE / substrate binding / complex | ||||||
Function / homology | Function and homology information cholest-4-en-3-one 26-monooxygenase activity / steroid hydroxylase activity / cholesterol catabolic process / iron ion binding / heme binding Similarity search - Function | ||||||
Biological species | Bacillus sonorensis L12 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.27 Å | ||||||
Authors | Shen, P.P. / Huang, J.-W. / Li, X. / Liu, W.D. / Chen, C.-C. / Guo, R.-T. | ||||||
Funding support | 1items
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Citation | Journal: Acs Catalysis / Year: 2023 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7y98.cif.gz | 170.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7y98.ent.gz | 133.4 KB | Display | PDB format |
PDBx/mmJSON format | 7y98.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7y98_validation.pdf.gz | 1.7 MB | Display | wwPDB validaton report |
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Full document | 7y98_full_validation.pdf.gz | 1.7 MB | Display | |
Data in XML | 7y98_validation.xml.gz | 32.1 KB | Display | |
Data in CIF | 7y98_validation.cif.gz | 43.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/y9/7y98 ftp://data.pdbj.org/pub/pdb/validation_reports/y9/7y98 | HTTPS FTP |
-Related structure data
Related structure data | 7y97C 7y9oC 4rm4S S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-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: 46490.848 Da / Num. of mol.: 2 / Mutation: C40Y,N49S,L264F Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacillus sonorensis L12 (bacteria) / Gene: BSONL12_06623 / Plasmid: pRSF-DuetI / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: M5PFT9 #2: Chemical | #3: Chemical | #4: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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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: SYNCHROTRON / Site: NSRRC / Beamline: BL15A1 / Wavelength: 1 Å |
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: 1 Å / Relative weight: 1 |
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 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT 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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