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Open data
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Basic information
Entry | Database: PDB / ID: 8dme | ||||||
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Title | CYP102A1 in Open Conformation | ||||||
![]() | Bifunctional cytochrome P450/NADPH--P450 reductase | ||||||
![]() | OXIDOREDUCTASE / cytochrome P450 electron transfer protein dynamic CYP102A1 | ||||||
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 | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 6.5 Å | ||||||
![]() | Su, M. / Xu, H. | ||||||
Funding support | 1items
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![]() | ![]() Title: Insight into the conformational dynamics of cytochrome P450 CYP102A1 enzyme using Cryo-EM Authors: Su, M. / Xu, H. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 428.4 KB | Display | ![]() |
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PDB format | ![]() | 336.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.7 MB | Display | ![]() |
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Full document | ![]() | 1.8 MB | Display | |
Data in XML | ![]() | 84.7 KB | Display | |
Data in CIF | ![]() | 117.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 27534MC ![]() 8dmgC M: map data used to model this data C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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1 |
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Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 116541.734 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Strain: ATCC 14581 / DSM 32 / CCUG 1817 / JCM 2506 / NBRC 15308 / NCIMB 9376 / NCTC 10342 / NRRL B-14308 / VKM B-512 / Ford 19 Gene: cyp102A1, cyp102, BG04_163 / Production host: ![]() ![]() References: UniProt: P14779, unspecific monooxygenase, NADPH-hemoprotein reductase |
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-Non-polymers , 6 types, 18 molecules ![](data/chem/img/HEM.gif)
![](data/chem/img/1C6.gif)
![](data/chem/img/FMN.gif)
![](data/chem/img/FAD.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/PG4.gif)
![](data/chem/img/1C6.gif)
![](data/chem/img/FMN.gif)
![](data/chem/img/FAD.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/PG4.gif)
#2: Chemical | #3: Chemical | #4: Chemical | #5: Chemical | #6: Chemical | ChemComp-SO4 / #7: Chemical | ChemComp-PG4 / |
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-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
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Sample preparation
Component | Name: CYP102A1 / Type: COMPLEX / Details: BM3 CYP102A / Entity ID: #1 / Source: RECOMBINANT |
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Molecular weight | Value: 0.24 MDa / Experimental value: YES |
Source (natural) | Organism: ![]() |
Source (recombinant) | Organism: ![]() ![]() |
Buffer solution | pH: 7.4 Details: Fresh prepare sodium phosphate (50mM) + potassium chloride (150mM), pH7.4 and filter with 0.22um filters. |
Buffer component | Conc.: 50 mM / Name: sodium phosphate + potassium chloride / Formula: K2HPO4-KH2PO4-KCL |
Specimen | Conc.: 5 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES Details: The CYP102A1 sample purify and concentrated to 5mg/ml. |
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE |
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Electron microscopy imaging
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: ![]() |
Electron lens | Mode: BRIGHT FIELD / Nominal defocus max: 2500 nm / Nominal defocus min: 1500 nm |
Image recording | Electron dose: 15 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) |
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Processing
CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION |
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3D reconstruction | Resolution: 6.5 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 204254 / Symmetry type: POINT |