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Yorodumi- PDB-1fzh: METHANE MONOOXYGENASE HYDROXYLASE, FORM II PRESSURIZED WITH XENON GAS -
+Open data
-Basic information
Entry | Database: PDB / ID: 1fzh | ||||||
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Title | METHANE MONOOXYGENASE HYDROXYLASE, FORM II PRESSURIZED WITH XENON GAS | ||||||
Components | (METHANE MONOOXYGENASE COMPONENT A, ...) x 3 | ||||||
Keywords | OXIDOREDUCTASE / dinuclear iron center / monooxygenase | ||||||
Function / homology | Function and homology information methane metabolic process / methane monooxygenase (soluble) / : / : / : / one-carbon metabolic process / metal ion binding Similarity search - Function | ||||||
Biological species | Methylococcus capsulatus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.6 Å | ||||||
Authors | Whittington, D.A. / Rosenzweig, A.C. / Frederick, C.A. / Lippard, S.J. | ||||||
Citation | Journal: Biochemistry / Year: 2001 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1fzh.cif.gz | 442.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1fzh.ent.gz | 360.3 KB | Display | PDB format |
PDBx/mmJSON format | 1fzh.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1fzh_validation.pdf.gz | 477.6 KB | Display | wwPDB validaton report |
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Full document | 1fzh_full_validation.pdf.gz | 521.8 KB | Display | |
Data in XML | 1fzh_validation.xml.gz | 81.9 KB | Display | |
Data in CIF | 1fzh_validation.cif.gz | 112.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fz/1fzh ftp://data.pdbj.org/pub/pdb/validation_reports/fz/1fzh | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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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) Methylococcus capsulatus (bacteria) 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) Methylococcus capsulatus (bacteria) 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) Methylococcus capsulatus (bacteria) References: UniProt: P11987, methane monooxygenase (soluble) |
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-Non-polymers , 4 types, 591 molecules
#4: Chemical | ChemComp-FE / #5: Chemical | ChemComp-CA / #6: Chemical | ChemComp-XE / #7: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.8 Å3/Da / Density % sol: 56 % | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7 Details: PEG 8000, CaCl2, MOPS, pH 7.0, VAPOR DIFFUSION, HANGING DROP at 277K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 1.08 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Apr 4, 1996 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.08 Å / Relative weight: 1 |
Reflection | Resolution: 2.6→30 Å / Num. all: 87646 / Num. obs: 81746 / % possible obs: 93.2 % / Observed criterion σ(I): 2 / Redundancy: 6.8 % / Biso Wilson estimate: 27.5 Å2 / Rmerge(I) obs: 0.105 / Net I/σ(I): 11.7 |
Reflection shell | Resolution: 2.6→2.69 Å / Redundancy: 2.3 % / Rmerge(I) obs: 0.281 / % possible all: 96.6 |
Reflection | *PLUS Num. measured all: 552751 |
Reflection shell | *PLUS % possible obs: 96.6 % |
-Processing
Software |
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Refinement | Resolution: 2.6→29 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 29746917.88 / 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: 29.19 Å2 / ksol: 0.313 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 31.8 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.6→29 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.6→2.76 Å / Rfactor Rfree error: 0.015 / 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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