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Yorodumi- PDB-1xvf: soluble methane monooxygenase hydroxylase: chloropropanol soaked ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1xvf | ||||||
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Title | soluble methane monooxygenase hydroxylase: chloropropanol soaked structure | ||||||
Components | (Methane monooxygenase component A ...) x 3 | ||||||
Keywords | OXIDOREDUCTASE / methane / diiron / four-helix bundle / cavities / product | ||||||
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 / MOLECULAR REPLACEMENT / Resolution: 2 Å | ||||||
Authors | Sazinsky, M.H. / Lippard, S.J. | ||||||
Citation | Journal: J.Am.Chem.Soc. / Year: 2005 Title: Product Bound Structures of the Soluble Methane Monooxygenase Hydroxylase from Methylococcus capsulatus (Bath): Protein Motion in the Alpha-Subunit Authors: Sazinsky, M.H. / 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 | 1xvf.cif.gz | 462 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1xvf.ent.gz | 372.8 KB | Display | PDB format |
PDBx/mmJSON format | 1xvf.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1xvf_validation.pdf.gz | 496.6 KB | Display | wwPDB validaton report |
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Full document | 1xvf_full_validation.pdf.gz | 540.8 KB | Display | |
Data in XML | 1xvf_validation.xml.gz | 91.3 KB | Display | |
Data in CIF | 1xvf_validation.cif.gz | 130.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xv/1xvf ftp://data.pdbj.org/pub/pdb/validation_reports/xv/1xvf | HTTPS FTP |
-Related structure data
Related structure data | 1xu3C 1xu5C 1xvbC 1xvcC 1xvdC 1xveC 1xvgC 1mtyS C: citing same article (ref.) S: Starting model for refinement |
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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 / Fragment: alpha subunit / 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 / Fragment: beta subunit / 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 / Fragment: gamma subunit / Source method: isolated from a natural source / Source: (natural) Methylococcus capsulatus (bacteria) References: UniProt: P11987, methane monooxygenase (soluble) |
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-Non-polymers , 3 types, 1296 molecules
#4: Chemical | ChemComp-FE / #5: Chemical | ChemComp-3CL / #6: 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: 2.3 Å3/Da / Density % sol: 55.1 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7 Details: MOPS, PEG 8000, NaN3, CaCl2, glycerol, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: May 1, 2002 |
Radiation | Monochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2→30 Å / Num. all: 180877 / Num. obs: 180877 / % possible obs: 99.4 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 4.3 % / Biso Wilson estimate: 14.4 Å2 / Rmerge(I) obs: 0.079 / Rsym value: 0.079 / Net I/σ(I): 14.2 |
Reflection shell | Resolution: 2→2.08 Å / Rmerge(I) obs: 0.364 / Mean I/σ(I) obs: 4 / Rsym value: 0.364 / % possible all: 97.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1mty Resolution: 2→19.98 Å / Rfactor Rfree error: 0.002 / Data cutoff high absF: 331410.4 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2 / σ(I): 2 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 55.3295 Å2 / ksol: 0.352393 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 31.1 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2→19.98 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2→2.08 Å / Rfactor Rfree error: 0.008 / Total num. of bins used: 6
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Xplor file |
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