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- PDB-6d7k: Complex structure of Methane monooxygenase hydroxylase in complex... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6d7k | |||||||||
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Title | Complex structure of Methane monooxygenase hydroxylase in complex with inhibitory subunit | |||||||||
![]() | (Methane monooxygenase hydroxylase, ...) x 4 | |||||||||
![]() | oxidoreductase/inhibitor / Complex / OXIDOREDUCTASE / oxidoreductase-inhibitor complex | |||||||||
Function / homology | ![]() methane monooxygenase [NAD(P)H] activity / methane metabolic process / oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, NAD(P)H as one donor, and incorporation of one atom of oxygen / : / monooxygenase activity Similarity search - Function | |||||||||
Biological species | ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Kim, H. / Lee, S.J. / Cho, U.-S. | |||||||||
Funding support | ![]() ![]()
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![]() | ![]() Title: MMOD-induced structural changes of hydroxylase in soluble methane monooxygenase. Authors: Kim, H. / An, S. / Park, Y.R. / Jang, H. / Yoo, H. / Park, S.H. / Lee, S.J. / Cho, U.S. #1: ![]() Title: The crystal structure of the MMOH-MMOD complex reveals the inhibitory mechanism of MMOD Authors: Kim, H. / Lee, S.J. / Cho, U.-S. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 446.3 KB | Display | ![]() |
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PDB format | ![]() | 357.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 523.7 KB | Display | ![]() |
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Full document | ![]() | 573.6 KB | Display | |
Data in XML | ![]() | 80.4 KB | Display | |
Data in CIF | ![]() | 110.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1mhyS S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
-Methane monooxygenase hydroxylase, ... , 4 types, 8 molecules AEBFCGDH
#1: Protein | Mass: 59979.230 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() #2: Protein | Mass: 45239.246 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() #3: Protein | Mass: 19379.207 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() #4: Protein | Mass: 12875.136 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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-Non-polymers , 4 types, 347 molecules ![](data/chem/img/FE.gif)
![](data/chem/img/HEZ.gif)
![](data/chem/img/FMT.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/HEZ.gif)
![](data/chem/img/FMT.gif)
![](data/chem/img/HOH.gif)
#5: Chemical | ChemComp-FE / #6: Chemical | #7: Chemical | #8: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.53 Å3/Da / Density % sol: 55.99 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 10% (w/v) PEG 8000, 20% (v/v) ethylene glycol, 0.02 M of alcohols mix (1,6-hexanediol, 1-butanol, (RS)-1,2-propanediol, 2-propanol, 1,4-butanediol, and 1,3-propanediol), 0.1 M MES/imidazole ...Details: 10% (w/v) PEG 8000, 20% (v/v) ethylene glycol, 0.02 M of alcohols mix (1,6-hexanediol, 1-butanol, (RS)-1,2-propanediol, 2-propanol, 1,4-butanediol, and 1,3-propanediol), 0.1 M MES/imidazole buffer (pH 6.5) and 1,3-butanediol |
-Data collection
Diffraction | Mean temperature: 273 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MAR CCD 130 mm / Detector: CCD / Date: Oct 20, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.987 Å / Relative weight: 1 |
Reflection | Resolution: 2.59→50 Å / Num. obs: 84164 / % possible obs: 99.5 % / Redundancy: 4.3 % / Rmerge(I) obs: 0.124 / Net I/σ(I): 12.8 |
Reflection shell | Resolution: 2.59→2.64 Å / Rmerge(I) obs: 0.793 / % possible all: 98.9 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1MHY Resolution: 2.6→22.289 Å / SU ML: 0.3 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 23.31
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.6→22.289 Å
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Refine LS restraints |
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LS refinement shell |
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