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- PDB-1fz8: METHANE MONOOXYGENASE HYDROXYLASE, FORM II COCRYSTALLIZED WITH DI... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1fz8 | ||||||
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Title | METHANE MONOOXYGENASE HYDROXYLASE, FORM II COCRYSTALLIZED WITH DIBROMOMETHANE | ||||||
![]() | (METHANE MONOOXYGENASE COMPONENT A, ...) x 3 | ||||||
![]() | OXIDOREDUCTASE / dinuclear iron center / monooxygenase | ||||||
Function / homology | ![]() methane metabolic process / methane monooxygenase (soluble) / : / : / : / one-carbon metabolic process / metal ion binding Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Whittington, D.A. / Rosenzweig, A.C. / Frederick, C.A. / Lippard, S.J. | ||||||
![]() | ![]() Title: Xenon and halogenated alkanes track putative substrate binding cavities in the soluble methane monooxygenase hydroxylase. Authors: Whittington, D.A. / Rosenzweig, A.C. / Frederick, C.A. / Lippard, S.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 | ![]() | 458.4 KB | Display | ![]() |
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PDB format | ![]() | 371.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 491.9 KB | Display | ![]() |
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Full document | ![]() | 536.8 KB | Display | |
Data in XML | ![]() | 87.8 KB | Display | |
Data in CIF | ![]() | 123.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related 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 COMPONENT A, ... , 3 types, 6 molecules ABCDEF
#1: Protein | Mass: 60719.113 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() References: UniProt: P22869, methane monooxygenase (soluble) #2: Protein | Mass: 45184.660 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() References: UniProt: P18798, methane monooxygenase (soluble) #3: Protein | Mass: 19879.732 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() References: UniProt: P11987, methane monooxygenase (soluble) |
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-Non-polymers , 4 types, 1086 molecules ![](data/chem/img/FE.gif)
![](data/chem/img/CA.gif)
![](data/chem/img/2BM.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/CA.gif)
![](data/chem/img/2BM.gif)
![](data/chem/img/HOH.gif)
#4: Chemical | ChemComp-FE / #5: Chemical | #6: Chemical | ChemComp-2BM / #7: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.69 Å3/Da / Density % sol: 54.3 % | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7 Details: PEG 8000, CaCl2, MOPS, 1,10-decanedioic acid, dibromomethane, pH 7.0, VAPOR DIFFUSION, HANGING DROP at 298K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Details: Whittington, D.A., (2001) J. Am. Chem. Soc., 123, 827. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Apr 2, 1998 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.08 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→30 Å / Num. all: 158927 / Num. obs: 136846 / % possible obs: 86 % / Observed criterion σ(I): 2 / Redundancy: 4.8 % / Biso Wilson estimate: 12.1 Å2 / Rmerge(I) obs: 0.084 / Net I/σ(I): 9.4 |
Reflection shell | Resolution: 2.1→2.14 Å / Redundancy: 2.4 % / Rmerge(I) obs: 0.555 / % possible all: 85.3 |
Reflection | *PLUS Num. measured all: 654647 |
Reflection shell | *PLUS % possible obs: 85.3 % |
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Processing
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Refinement | Resolution: 2.1→23.5 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 18755402.69 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 54.59 Å2 / ksol: 0.358 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 28.5 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.1→23.5 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.1→2.23 Å / Rfactor Rfree error: 0.013 / Total num. of bins used: 6
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Xplor file |
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Software | *PLUS Name: CNS / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Lowest resolution: 30 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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