+Open data
-Basic information
Entry | Database: PDB / ID: 1fz1 | ||||||
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Title | METHANE MONOOXYGENASE HYDROXYLASE, FORM III OXIDIZED | ||||||
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: 1.96 Å | ||||||
Authors | Whittington, D.A. / Lippard, S.J. | ||||||
Citation | Journal: J.Am.Chem.Soc. / Year: 2001 Title: Crystal structures of the soluble methane monooxygenase hydroxylase from Methylococcus capsulatus (Bath) demonstrating geometrical variability at the dinuclear iron active site. Authors: Whittington, D.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 | 1fz1.cif.gz | 464.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1fz1.ent.gz | 375.7 KB | Display | PDB format |
PDBx/mmJSON format | 1fz1.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1fz1_validation.pdf.gz | 489 KB | Display | wwPDB validaton report |
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Full document | 1fz1_full_validation.pdf.gz | 529.1 KB | Display | |
Data in XML | 1fz1_validation.xml.gz | 89.1 KB | Display | |
Data in CIF | 1fz1_validation.cif.gz | 128.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fz/1fz1 ftp://data.pdbj.org/pub/pdb/validation_reports/fz/1fz1 | HTTPS FTP |
-Related structure data
Related structure data | 1fyzC 1fz0C 1fz2C 1fz3C 1fz4C 1fz5C C: citing same article (ref.) |
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Similar 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, 1350 molecules
#4: Chemical | ChemComp-FE / #5: Chemical | ChemComp-CA / #6: Chemical | ChemComp-FMT / | #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: 2.7 Å3/Da / Density % sol: 54.45 % | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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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, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 98 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL9-1 / Wavelength: 0.98 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Apr 18, 1999 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 |
Reflection | Resolution: 1.96→30 Å / Num. all: 195655 / Num. obs: 194787 / % possible obs: 99.5 % / Observed criterion σ(I): 2 / Redundancy: 8.4 % / Biso Wilson estimate: 14 Å2 / Rmerge(I) obs: 0.067 / Net I/σ(I): 17.3 |
Reflection shell | Resolution: 1.96→1.99 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.362 / % possible all: 96.7 |
Reflection | *PLUS Num. measured all: 1641424 |
Reflection shell | *PLUS % possible obs: 96.7 % / Mean I/σ(I) obs: 4 |
-Processing
Software |
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Refinement | Resolution: 1.96→22.8 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 35544392.38 / 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: 51.14 Å2 / ksol: 0.359 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 30.1 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.96→22.8 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.96→2.08 Å / Rfactor Rfree error: 0.011 / 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: 22.8 Å / σ(F): 0 / % reflection Rfree: 3.5 % / Rfactor obs: 0.2 / Rfactor Rwork: 0.2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS Biso mean: 30.1 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor Rfree: 0.344 / % reflection Rfree: 3.5 % / Rfactor Rwork: 0.316 |