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- PDB-6m2i: Structure of the 2-Aminoisobutyric acid Monooxygenase Hydroxylase -
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Open data
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Basic information
Entry | Database: PDB / ID: 6m2i | ||||||
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Title | Structure of the 2-Aminoisobutyric acid Monooxygenase Hydroxylase | ||||||
![]() | (Amidohydrolase) x 2 | ||||||
![]() | OXIDOREDUCTASE / Monooxygenase / Hydroxylase | ||||||
Function / homology | ![]() secondary metabolic process / : / : / carboxy-lyase activity / hydrolase activity / metal ion binding / cytosol Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Hibi, M. / Mikami, B. / Ogawa, J. | ||||||
![]() | ![]() Title: A three-component monooxygenase from Rhodococcus wratislaviensis may expand industrial applications of bacterial enzymes. Authors: Hibi, M. / Fukuda, D. / Kenchu, C. / Nojiri, M. / Hara, R. / Takeuchi, M. / Aburaya, S. / Aoki, W. / Mizutani, K. / Yasohara, Y. / Ueda, M. / Mikami, B. / Takahashi, S. / Ogawa, J. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 196.8 KB | Display | ![]() |
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PDB format | ![]() | 125.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 3.7 MB | Display | ![]() |
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Full document | ![]() | 3.7 MB | Display | |
Data in XML | ![]() | 28.5 KB | Display | |
Data in CIF | ![]() | 40 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6m1wSC 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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Unit cell |
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Components on special symmetry positions |
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Components
-Protein , 2 types, 2 molecules AB
#1: Protein | Mass: 43474.820 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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#2: Protein | Mass: 42600.473 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
-Non-polymers , 5 types, 149 molecules ![](data/chem/img/ZN.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/FE.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/FE.gif)
![](data/chem/img/HOH.gif)
#3: Chemical | ChemComp-ZN / | ||||||
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#4: Chemical | ChemComp-SO4 / #5: Chemical | ChemComp-EDO / #6: Chemical | #7: Water | ChemComp-HOH / | |
-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.41 Å3/Da / Density % sol: 63.92 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: 0.1 M Tris/HCl (pH 8.5), 1 M ammonium sulfate and 12% (v/v) glycerol |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS EIGER R 4M / Detector: PIXEL / Date: Jan 31, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.45→45.92 Å / Num. obs: 207203 / % possible obs: 96.8 % / Redundancy: 2.56 % / Biso Wilson estimate: 40.25 Å2 / CC1/2: 0.994 / Rmerge(I) obs: 0.089 / Rrim(I) all: 0.113 / Net I/σ(I): 9.2 |
Reflection shell | Resolution: 2.45→2.6 Å / Redundancy: 2.64 % / Rmerge(I) obs: 0.471 / Mean I/σ(I) obs: 1.98 / Num. unique obs: 13330 / CC1/2: 0.709 / Rrim(I) all: 0.593 / % possible all: 98.9 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 6M1W Resolution: 2.45→44.99 Å / SU ML: 0.2704 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 23.5781
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 42.46 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.45→44.99 Å
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Refine LS restraints |
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LS refinement shell |
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