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- PDB-7m8r: Complex structure of Methane monooxygenase hydroxylase and regula... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7m8r | ||||||||||||
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Title | Complex structure of Methane monooxygenase hydroxylase and regulatory subunit with fluorosubstituted tryptophans | ||||||||||||
![]() | (Methane monooxygenase ...) x 4 | ||||||||||||
![]() | OXIDOREDUCTASE | ||||||||||||
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 / metal ion binding Similarity search - Function | ||||||||||||
Biological species | ![]() | ||||||||||||
Method | ![]() ![]() ![]() | ||||||||||||
![]() | Johns, J.C. / Banerjee, R. / Shi, K. / Semonis, M.M. / Aihara, H. / Pomerantz, W.C.K. / Lipscomb, J.D. | ||||||||||||
Funding support | ![]()
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![]() | ![]() Title: Soluble Methane Monooxygenase Component Interactions Monitored by 19 F NMR. Authors: Jones, J.C. / Banerjee, R. / Shi, K. / Semonis, M.M. / Aihara, H. / Pomerantz, W.C.K. / Lipscomb, J.D. | ||||||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 539.4 KB | Display | ![]() |
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PDB format | ![]() | 428.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 535.2 KB | Display | ![]() |
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Full document | ![]() | 546.3 KB | Display | |
Data in XML | ![]() | 100 KB | Display | |
Data in CIF | ![]() | 145.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7m8qC ![]() 6vk5S 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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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments:
NCS ensembles :
NCS oper:
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Components
-Methane monooxygenase ... , 4 types, 8 molecules AEBFCGDH
#1: Protein | Mass: 58971.008 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Gene: CQW49_12480 / Production host: ![]() ![]() #2: Protein | Mass: 44948.941 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Gene: CQW49_12475 / Production host: ![]() ![]() #3: Protein | Mass: 19313.203 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Gene: CQW49_12465 / Production host: ![]() ![]() #4: Protein | Mass: 14688.556 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Gene: CQW49_12470 / Production host: ![]() ![]() |
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-Non-polymers , 6 types, 1811 molecules ![](data/chem/img/FE.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/BEZ.gif)
![](data/chem/img/W6X.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/BEZ.gif)
![](data/chem/img/W6X.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/HOH.gif)
#5: Chemical | ChemComp-FE / #6: Chemical | ChemComp-EDO / #7: Chemical | #8: Chemical | #9: Chemical | ChemComp-CL / | #10: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | N |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.94 Å3/Da / Density % sol: 58.14 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / Details: TACSIMATE AND PEG3350 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Mar 7, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9791 Å / Relative weight: 1 |
Reflection | Resolution: 2.22→149.09 Å / Num. obs: 158676 / % possible obs: 99 % / Redundancy: 5.1 % / Biso Wilson estimate: 37.37 Å2 / Rmerge(I) obs: 0.139 / Net I/σ(I): 8.9 |
Reflection shell | Resolution: 2.22→2.25 Å / Redundancy: 4.8 % / Rmerge(I) obs: 1.05 / Num. unique obs: 4778 / % possible all: 93.7 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 6VK5 Resolution: 2.22→86.1 Å / SU ML: 0.23 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 20.28 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 107.59 Å2 / Biso mean: 39.37 Å2 / Biso min: 17.71 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.22→86.1 Å
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Refine LS restraints NCS |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 30
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