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Yorodumi- PDB-6ly4: The crystal structure of the BM3 mutant LG-23 in complex with tes... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6ly4 | |||||||||
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Title | The crystal structure of the BM3 mutant LG-23 in complex with testosterone | |||||||||
Components | Bifunctional cytochrome P450/NADPH--P450 reductase | |||||||||
Keywords | OXIDOREDUCTASE / P450-BM3 mutant / regio- and stereoselectivity / hydroxylation / testosterone | |||||||||
Function / homology | Function and homology information NADPH-hemoprotein reductase / NADPH-hemoprotein reductase activity / oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, reduced flavin or flavoprotein as one donor, and incorporation of one atom of oxygen / unspecific monooxygenase / aromatase activity / metabolic process / response to hormone / FMN binding / flavin adenine dinucleotide binding / iron ion binding ...NADPH-hemoprotein reductase / NADPH-hemoprotein reductase activity / oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, reduced flavin or flavoprotein as one donor, and incorporation of one atom of oxygen / unspecific monooxygenase / aromatase activity / metabolic process / response to hormone / FMN binding / flavin adenine dinucleotide binding / iron ion binding / heme binding / identical protein binding / cytosol Similarity search - Function | |||||||||
Biological species | Bacillus megaterium (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.68 Å | |||||||||
Authors | Peng, Y. / Chen, J. / Zhou, J. / Li, A. / ReetZ, M.T. | |||||||||
Citation | Journal: Angew.Chem.Int.Ed.Engl. / Year: 2020 Title: Regio- and Stereoselective Steroid Hydroxylation at C7 by Cytochrome P450 Monooxygenase Mutants. Authors: Li, A. / Acevedo-Rocha, C.G. / D'Amore, L. / Chen, J. / Peng, Y. / Garcia-Borras, M. / Gao, C. / Zhu, J. / Rickerby, H. / Osuna, S. / Zhou, J. / Reetz, M.T. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6ly4.cif.gz | 269.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6ly4.ent.gz | 178.4 KB | Display | PDB format |
PDBx/mmJSON format | 6ly4.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6ly4_validation.pdf.gz | 1.1 MB | Display | wwPDB validaton report |
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Full document | 6ly4_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 6ly4_validation.xml.gz | 24 KB | Display | |
Data in CIF | 6ly4_validation.cif.gz | 36.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ly/6ly4 ftp://data.pdbj.org/pub/pdb/validation_reports/ly/6ly4 | HTTPS FTP |
-Related structure data
Related structure data | 4kpaS S: Starting model for refinement |
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Similar structure data |
-Links
-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
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 55391.805 Da / Num. of mol.: 1 Mutation: R47W/S72W/F77Y/V78L/F81I/A82L/F87G/T88S/M17T/M185Q/L188Q/I209T/A328G/A330W Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacillus megaterium (strain ATCC 14581 / DSM 32 / JCM 2506 / NBRC 15308 / NCIMB 9376 / NCTC 10342 / VKM B-512) (bacteria) Gene: cyp102A1, cyp102, BG04_163 / Production host: Escherichia coli BL21(DE3) (bacteria) References: UniProt: P14779, unspecific monooxygenase, NADPH-hemoprotein reductase |
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-Non-polymers , 5 types, 477 molecules
#2: Chemical | ChemComp-TES / | ||||
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#3: Chemical | ChemComp-IMD / | ||||
#4: Chemical | ChemComp-EDO / #5: Chemical | ChemComp-HEM / | #6: Water | ChemComp-HOH / | |
-Details
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: 2.29 Å3/Da / Density % sol: 46.24 % |
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Crystal grow | Temperature: 289.15 K / Method: vapor diffusion, sitting drop Details: 10% w/v PEG 20000, 20% v/v PEG MME 550, 0.03 M of each ethylene glycol (0.3M diethyleneglycol, 0.3M triethyleneglycol, 0.3M tetraethyleneglycol, 0.3 M pentaethyleneglycol), 0.1M MES/imidazole pH 6.5 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97892 Å |
Detector | Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Jan 12, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97892 Å / Relative weight: 1 |
Reflection | Resolution: 1.68→50 Å / Num. obs: 57404 / % possible obs: 100 % / Redundancy: 6.7 % / Biso Wilson estimate: 13.89 Å2 / CC1/2: 0.72 / Net I/σ(I): 34.294 |
Reflection shell | Resolution: 1.68→1.71 Å / Num. unique obs: 57404 / CC1/2: 0.715 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4kpa Resolution: 1.68→41.6 Å / SU ML: 0.1603 / Cross valid method: NONE / σ(F): 1.35 / Phase error: 17.7929 / Stereochemistry target values: GeoStd + Monomer Library
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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 mean: 22.74 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.68→41.6 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Origin x: 17.8363142091 Å / Origin y: 20.6739281147 Å / Origin z: -71.1777692831 Å
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Refinement TLS group | Selection details: all |