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- PDB-6k9s: Structure of the Carbonylruthenium Mesoporphyrin IX-Reconstituted... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6k9s | ||||||
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Title | Structure of the Carbonylruthenium Mesoporphyrin IX-Reconstituted CYP102A1 Haem Domain with N-Abietoyl-L-Tryptophan | ||||||
![]() | Bifunctional cytochrome P450/NADPH--P450 reductase | ||||||
![]() | OXIDOREDUCTASE / Monooxygenase | ||||||
Function / homology | ![]() 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 | ![]() | ||||||
Method | ![]() ![]() ![]() ![]() | ||||||
![]() | Stanfield, J.K. / Omura, K. / Kasai, C. / Sugimoto, H. / Shiro, Y. / Watanabe, Y. / Shoji, O. | ||||||
Funding support | ![]()
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![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 429.3 KB | Display | ![]() |
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PDB format | ![]() | 350.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 2.3 MB | Display | ![]() |
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Full document | ![]() | 2.3 MB | Display | |
Data in XML | ![]() | 43.9 KB | Display | |
Data in CIF | ![]() | 62.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6jlvC ![]() 6jmhC ![]() 6jmwC ![]() 6jo1C ![]() 6js8C ![]() 6jvcC ![]() 6jzsC ![]() 6k24C ![]() 6k58C ![]() 3wspS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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2 | ![]()
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: HOH / Beg label comp-ID: HOH / End auth comp-ID: HOH / End label comp-ID: HOH / Refine code: 1 / Auth seq-ID: 601
NCS oper:
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Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 52300.660 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: P14779, unspecific monooxygenase, NADPH-hemoprotein reductase |
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-Non-polymers , 5 types, 583 molecules ![](data/chem/img/RUR.gif)
![](data/chem/img/CMO.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/WAA.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/CMO.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/WAA.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | #3: Chemical | #4: Chemical | ChemComp-GOL / #5: Chemical | #6: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.75 Å3/Da / Density % sol: 55.2 % |
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Crystal grow | Temperature: 293 K / Method: batch mode Details: PEG 8000, 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: ![]() ![]() ![]() | |||||||||||||||||||||||||||
Detector | Type: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Jan 25, 2019 | |||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 | |||||||||||||||||||||||||||
Reflection | Resolution: 1.55→48.73 Å / Num. obs: 165527 / % possible obs: 100 % / Redundancy: 10.6 % / CC1/2: 0.999 / Rmerge(I) obs: 0.094 / Rpim(I) all: 0.03 / Rrim(I) all: 0.099 / Net I/σ(I): 11 / Num. measured all: 1752390 / Scaling rejects: 24 | |||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Phasing
Phasing | Method: ![]() | ||||||
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Phasing MR | R rigid body: 0.511
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 3WSP Resolution: 1.55→46.49 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.963 / SU B: 3.618 / SU ML: 0.057 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.086 / ESU R Free: 0.075 Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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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 max: 110.36 Å2 / Biso mean: 29.858 Å2 / Biso min: 13 Å2
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Refinement step | Cycle: final / Resolution: 1.55→46.49 Å
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Refine LS restraints |
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Refine LS restraints NCS | Number: 74 / Type: TIGHT THERMAL / Rms dev position: 5.89 Å / Weight position: 0.5 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 1.55→1.59 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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