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Yorodumi- PDB-1fzi: METHANE MONOOXYGENASE HYDROXYLASE, FORM I PRESSURIZED WITH XENON GAS -
+Open data
-Basic information
Entry | Database: PDB / ID: 1fzi | ||||||
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Title | METHANE MONOOXYGENASE HYDROXYLASE, FORM I PRESSURIZED WITH XENON GAS | ||||||
Components |
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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: 3.3 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 | 1fzi.cif.gz | 406 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1fzi.ent.gz | 331.8 KB | Display | PDB format |
PDBx/mmJSON format | 1fzi.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1fzi_validation.pdf.gz | 470.9 KB | Display | wwPDB validaton report |
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Full document | 1fzi_full_validation.pdf.gz | 512.6 KB | Display | |
Data in XML | 1fzi_validation.xml.gz | 70.5 KB | Display | |
Data in CIF | 1fzi_validation.cif.gz | 96.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fz/1fzi ftp://data.pdbj.org/pub/pdb/validation_reports/fz/1fzi | 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
#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) #4: Chemical | ChemComp-FE / #5: Chemical | ChemComp-XE / |
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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: 2.22 Å3/Da / Density % sol: 44.55 % | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7 Details: PEG 4000, ammonium acetate, Li2SO4, MOPS, pH 7.0, VAPOR DIFFUSION, HANGING DROP at 277K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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: 3.3→12 Å / Num. all: 33934 / Num. obs: 25369 / % possible obs: 74 % / Observed criterion σ(I): 2 / Redundancy: 13.4 % / Rmerge(I) obs: 0.111 |
Reflection shell | Highest resolution: 3.3 Å / Rmerge(I) obs: 0.219 / % possible all: 69.9 |
Reflection | *PLUS Num. measured all: 340070 |
Reflection shell | *PLUS % possible obs: 69.9 % |
-Processing
Software |
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Refinement | Resolution: 3.3→12 Å / Rfactor Rfree error: 0.008 / Data cutoff high absF: 233591164.9 / 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: 10 Å2 / ksol: 0.36 e/Å3 | |||||||||||||||||||||||||
Displacement parameters | Biso mean: 11.1 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 3.3→12 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 3.3→3.5 Å / Rfactor Rfree error: 0.02 / Total num. of bins used: 6
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Xplor file |
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Software | *PLUS Name: CNS / Classification: refinement | |||||||||||||||||||||||||
Refinement | *PLUS | |||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||
Refine LS restraints | *PLUS
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