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Yorodumi- PDB-8hg9: Cytochrome P450 steroid hydroxylase (BaCYP106A6) from Bacillus species -
+Open data
-Basic information
Entry | Database: PDB / ID: 8hg9 | ||||||
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Title | Cytochrome P450 steroid hydroxylase (BaCYP106A6) from Bacillus species | ||||||
Components | cytochrome P450 steroid hydroxylase | ||||||
Keywords | HORMONE / cytochrome P450 / steroid hydroxylase | ||||||
Function / homology | Function and homology information oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen / monooxygenase activity / iron ion binding / heme binding Similarity search - Function | ||||||
Biological species | Bacillus sp. (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.79 Å | ||||||
Authors | Do, H. / Lee, J.H. | ||||||
Funding support | Korea, Republic Of, 1items
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Citation | Journal: J Microbiol Biotechnol. / Year: 2023 Title: Crystal Structure and Biochemical Analysis of a Cytochrome P450 Steroid Hydroxylase ( Ba CYP106A6) from Bacillus Species. Authors: Kim, K.H. / Do, H. / Lee, C.W. / Subedi, P. / Choi, M. / Nam, Y. / Lee, J.H. / Oh, T.J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8hg9.cif.gz | 388.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8hg9.ent.gz | 264.7 KB | Display | PDB format |
PDBx/mmJSON format | 8hg9.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/hg/8hg9 ftp://data.pdbj.org/pub/pdb/validation_reports/hg/8hg9 | HTTPS FTP |
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-Related structure data
Similar structure data | Similarity search - Function & homologyF&H Search |
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-Links
-Assembly
Deposited unit |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Ens-ID: ens_1
NCS oper: (Code: givenMatrix: (0.823594358578, -0.00756553691591, -0.567128817086), (-0.00472883291139, -0.999967872924, 0.00647234567927), (-0.567159563666, -0.00264872997298, -0.82360367506)Vector: ...NCS oper: (Code: given Matrix: (0.823594358578, -0.00756553691591, -0.567128817086), Vector: |
-Components
#1: Protein | Mass: 47188.406 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacillus sp. (in: Bacteria) (bacteria) / Gene: HMPREF1013_04413 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: E5WPM6 #2: Chemical | #3: 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: 2.6 Å3/Da / Density % sol: 52.7 % |
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Crystal grow | Temperature: 295 K / Method: evaporation Details: 0.18 M Ammonium Citrate Dibasic, 22% (w/v) PEG 3350 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: PAL/PLS / Beamline: 5C (4A) / Wavelength: 0.9794 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 12, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9794 Å / Relative weight: 1 |
Reflection | Resolution: 2.79→50 Å / Num. obs: 22227 / % possible obs: 99.1 % / Redundancy: 6.4 % / Biso Wilson estimate: 41.83 Å2 / CC1/2: 1 / Net I/σ(I): 31 |
Reflection shell | Resolution: 2.8→2.94 Å / Num. unique obs: 3161 / CC1/2: 1 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: modeling Resolution: 2.79→37.59 Å / SU ML: 0.3851 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 30.3598 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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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: 42.64 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.79→37.59 Å
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Refine LS restraints |
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Refine LS restraints NCS | Type: Torsion NCS / Rms dev position: 0.752308103054 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
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Refinement TLS params. | Method: refined / Origin x: 15.7362270893 Å / Origin y: -23.9366767547 Å / Origin z: 19.6696944555 Å
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Refinement TLS group | Selection details: all |