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Yorodumi- PDB-8hkj: Crystal structure of the CYP102A5 haem Domain isolated from Bacil... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8hkj | |||||||||||||||
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Title | Crystal structure of the CYP102A5 haem Domain isolated from Bacillus cereus | |||||||||||||||
Components | Bifunctional cytochrome P450/NADPH--P450 reductase | |||||||||||||||
Keywords | OXIDOREDUCTASE / Cytochrome P450 / Monooxygenase | |||||||||||||||
Function / homology | Function and homology information NADPH-hemoprotein reductase / NADPH-hemoprotein reductase activity / unspecific monooxygenase / aromatase activity / FMN binding / iron ion binding / heme binding Similarity search - Function | |||||||||||||||
Biological species | Bacillus cereus (bacteria) | |||||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å | |||||||||||||||
Authors | Stanfield, J.K. / Onoda, H. / Sugimoto, H. / Shoji, O. | |||||||||||||||
Funding support | Japan, 4items
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Citation | Journal: J.Inorg.Biochem. / Year: 2023 Title: Investigating the applicability of the CYP102A1-decoy-molecule system to other members of the CYP102A subfamily. Authors: Stanfield, J.K. / Onoda, H. / Ariyasu, S. / Kasai, C. / Burfoot, E.M. / Sugimoto, H. / Shoji, O. | |||||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8hkj.cif.gz | 988.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8hkj.ent.gz | 828.4 KB | Display | PDB format |
PDBx/mmJSON format | 8hkj.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8hkj_validation.pdf.gz | 6.7 MB | Display | wwPDB validaton report |
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Full document | 8hkj_full_validation.pdf.gz | 6.6 MB | Display | |
Data in XML | 8hkj_validation.xml.gz | 182.7 KB | Display | |
Data in CIF | 8hkj_validation.cif.gz | 234.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/hk/8hkj ftp://data.pdbj.org/pub/pdb/validation_reports/hk/8hkj | HTTPS FTP |
-Related structure data
Related structure data | 2ij2S S: Starting model for refinement |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
-Components
#1: Protein | Mass: 52925.570 Da / Num. of mol.: 12 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacillus cereus (bacteria) / Gene: BKK64_01385 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A853ZNE6 #2: Chemical | ChemComp-HEM / #3: Chemical | ChemComp-PLM / Has ligand of interest | N | |
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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: 2.65 Å3/Da / Density % sol: 53.66 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.95 / Details: 70 mM MgCl2, 4.75% PEG8000, 50 mM Tris |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B2 / Wavelength: 1 Å |
Detector | Type: RAYONIX MX225-HS / Detector: CCD / Date: Nov 9, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.8→91.18 Å / Num. obs: 157761 / % possible obs: 98.1 % / Redundancy: 2 % / CC1/2: 0.995 / Rmerge(I) obs: 0.058 / Rpim(I) all: 0.058 / Rrim(I) all: 0.082 / Net I/σ(I): 5 / Num. measured all: 312136 |
Reflection shell | Resolution: 2.8→2.85 Å / % possible obs: 97.5 % / Redundancy: 2 % / Rmerge(I) obs: 0.582 / Num. measured all: 15467 / Num. unique obs: 7830 / CC1/2: 0.52 / Rpim(I) all: 0.582 / Rrim(I) all: 0.823 / Net I/σ(I) obs: 1.1 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2IJ2 Resolution: 2.8→19.96 Å / SU ML: 0.41 / Cross valid method: THROUGHOUT / σ(F): 0.24 / Phase error: 30.04 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.8→19.96 Å
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Refine LS restraints |
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LS refinement shell |
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