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Yorodumi- PDB-1fz4: METHANE MONOOXYGENASE HYDROXYLASE, FORM III SOAKED AT PH 8.5 (0.1... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1fz4 | ||||||
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Title | METHANE MONOOXYGENASE HYDROXYLASE, FORM III SOAKED AT PH 8.5 (0.1 M TRIS) | ||||||
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: 2.38 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 | 1fz4.cif.gz | 440.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1fz4.ent.gz | 359.3 KB | Display | PDB format |
PDBx/mmJSON format | 1fz4.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1fz4_validation.pdf.gz | 490.2 KB | Display | wwPDB validaton report |
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Full document | 1fz4_full_validation.pdf.gz | 545.5 KB | Display | |
Data in XML | 1fz4_validation.xml.gz | 82 KB | Display | |
Data in CIF | 1fz4_validation.cif.gz | 111.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fz/1fz4 ftp://data.pdbj.org/pub/pdb/validation_reports/fz/1fz4 | HTTPS FTP |
-Related structure data
Related structure data | 1fyzC 1fz0C 1fz1C 1fz2C 1fz3C 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, 481 molecules
#4: Chemical | ChemComp-FE / #5: Chemical | #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: 2.68 Å3/Da / Density % sol: 54.07 % | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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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 at 298 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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: BL7-1 / Wavelength: 1.08 |
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: 2.38→30 Å / Num. all: 109126 / Num. obs: 103150 / % possible obs: 91.5 % / Observed criterion σ(I): 2 / Redundancy: 8 % / Biso Wilson estimate: 17.8 Å2 / Rmerge(I) obs: 0.084 / Net I/σ(I): 11.6 |
Reflection shell | Resolution: 2.38→2.42 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.503 / % possible all: 80.2 |
Reflection | *PLUS Num. measured all: 820337 |
Reflection shell | *PLUS % possible obs: 80.2 % / Mean I/σ(I) obs: 2.4 |
-Processing
Software |
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Refinement | Resolution: 2.38→29.7 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 16804725.76 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber / Details: BULK SOLVENT MODEL USED
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 33.13 Å2 / ksol: 0.341 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 43.9 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.38→29.7 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.38→2.53 Å / Rfactor Rfree error: 0.017 / Total num. of bins used: 6
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Xplor file |
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Software | *PLUS Name: CNS / Version: 1 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Lowest resolution: 29.7 Å / σ(F): 0 / % reflection Rfree: 3.5 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS Biso mean: 43.9 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor Rfree: 0.353 / % reflection Rfree: 3.5 % / Rfactor Rwork: 0.328 |