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Yorodumi- PDB-1fz9: Methane monooxygenase hydroxylase, form II cocrystallized with io... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1fz9 | ||||||
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Title | Methane monooxygenase hydroxylase, form II cocrystallized with iodoethane | ||||||
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: 2.3 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 | 1fz9.cif.gz | 450.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1fz9.ent.gz | 366.6 KB | Display | PDB format |
PDBx/mmJSON format | 1fz9.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1fz9_validation.pdf.gz | 496.8 KB | Display | wwPDB validaton report |
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Full document | 1fz9_full_validation.pdf.gz | 564.9 KB | Display | |
Data in XML | 1fz9_validation.xml.gz | 88.9 KB | Display | |
Data in CIF | 1fz9_validation.cif.gz | 121.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fz/1fz9 ftp://data.pdbj.org/pub/pdb/validation_reports/fz/1fz9 | 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, 792 molecules
#4: Chemical | ChemComp-FE / #5: Chemical | #6: Chemical | ChemComp-ETI / #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: 54.36 % | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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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, iodoethane. 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: 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: 2.3→30 Å / Num. all: 121481 / Num. obs: 107645 / % possible obs: 86.8 % / Observed criterion σ(I): 2 / Redundancy: 8.5 % / Biso Wilson estimate: 19.1 Å2 / Rmerge(I) obs: 0.078 / Net I/σ(I): 13 |
Reflection shell | Resolution: 2.3→2.37 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.404 / % possible all: 83.9 |
Reflection | *PLUS Num. measured all: 919602 |
Reflection shell | *PLUS % possible obs: 83.9 % |
-Processing
Software |
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Refinement | Resolution: 2.3→30 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 235356343.14 / 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: 45.54 Å2 / ksol: 0.348 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 43.8 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.3→30 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.3→2.44 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 Rfactor Rfree: 0.259 / Rfactor Rwork: 0.205 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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