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Yorodumi- PDB-6jmw: Structure of the Chromium Protoporphyrin IX-Reconstituted CYP102A... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6jmw | ||||||
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Title | Structure of the Chromium Protoporphyrin IX-Reconstituted CYP102A1 Haem Domain with N-Abietoyl-L-Tryptophan | ||||||
Components | Bifunctional cytochrome P450/NADPH--P450 reductase | ||||||
Keywords | OXIDOREDUCTASE / Monooxygenase | ||||||
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 / FMN binding / iron ion binding / heme binding / identical protein binding / cytoplasm Similarity search - Function | ||||||
Biological species | Bacillus megaterium (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 Å | ||||||
Authors | Stanfield, J.K. / Omura, K. / Kasai, C. / Sugimoto, H. / Shiro, Y. / Watanabe, Y. / Shoji, O. | ||||||
Funding support | Japan, 1items
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Citation | Journal: Angew.Chem.Int.Ed.Engl. / Year: 2020 Title: Crystals in Minutes: Instant On-Site Microcrystallisation of Various Flavours of the CYP102A1 (P450BM3) Haem Domain. Authors: Stanfield, J.K. / Omura, K. / Matsumoto, A. / Kasai, C. / Sugimoto, H. / Shiro, Y. / Watanabe, Y. / Shoji, O. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6jmw.cif.gz | 214.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6jmw.ent.gz | 169.1 KB | Display | PDB format |
PDBx/mmJSON format | 6jmw.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/jm/6jmw ftp://data.pdbj.org/pub/pdb/validation_reports/jm/6jmw | HTTPS FTP |
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-Related structure data
Related structure data | 6jlvC 6jmhC 6jo1C 6js8C 6jvcC 6jzsC 6k24C 6k58C 6k9sC 3wspS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 56253.945 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Details: CYP102A1 haem domain containing a C-terminal Sortase recognition sequence, and an N-terminal hexahistidine tag, which is followed by both a Thrombin and TEV protease cleavage Site. Source: (gene. exp.) Bacillus megaterium (bacteria) / Gene: cyp102A1 / Production host: Escherichia coli (E. coli) References: UniProt: P14779, unspecific monooxygenase, NADPH-hemoprotein reductase #2: Chemical | #3: Chemical | #4: Chemical | ChemComp-GOL / #5: Water | ChemComp-HOH / | |
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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: 2.44 Å3/Da / Density % sol: 49.55 % |
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Crystal grow | Temperature: 293 K / Method: batch mode Details: PEG8000, Magnesium Chloride, Tris-HCl, 0.5% DMSO, 125 uM N-Abietoyl-L-Tryptophan |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B1 / Wavelength: 1 Å |
Detector | Type: DECTRIS EIGER X 4M / Detector: PIXEL / Date: Oct 11, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.85→48.02 Å / Num. obs: 90862 / % possible obs: 98.9 % / Redundancy: 6.8 % / Rmerge(I) obs: 0.104 / Net I/σ(I): 10.6 |
Reflection shell | Resolution: 1.85→1.88 Å / Redundancy: 7.1 % / Rmerge(I) obs: 1.824 / Mean I/σ(I) obs: 1.2 / % possible all: 98.7 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3WSP Resolution: 1.85→48.02 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.95 / SU B: 4.069 / SU ML: 0.113 / Cross valid method: THROUGHOUT / ESU R: 0.135 / ESU R Free: 0.128 / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 33.52 Å2
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Refinement step | Cycle: LAST / Resolution: 1.85→48.02 Å
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Refine LS restraints |
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