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Yorodumi- PDB-1xmf: Structure of Mn(II)-Soaked Apo Methane Monooxygenase Hydroxylase ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1xmf | ||||||
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Title | Structure of Mn(II)-Soaked Apo Methane Monooxygenase Hydroxylase Crystals from M. capsulatus (Bath) | ||||||
Components | (Methane monooxygenase component A ...) x 3 | ||||||
Keywords | OXIDOREDUCTASE / dimanganese / MMOH / diiron / methane / four-helix bundle | ||||||
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: 2.32 Å | ||||||
Authors | Sazinsky, M.H. / Merkx, M. / Cadieux, E. / Tang, S. / Lippard, S.J. | ||||||
Citation | Journal: Biochemistry / Year: 2004 Title: Preparation and X-ray Structures of Metal-Free, Dicobalt and Dimanganese Forms of Soluble Methane Monooxygenase Hydroxylase from Methylococcus capsulatus (Bath) Authors: Sazinsky, M.H. / Merkx, M. / Cadieux, E. / Tang, S. / 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 | 1xmf.cif.gz | 456.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1xmf.ent.gz | 368.8 KB | Display | PDB format |
PDBx/mmJSON format | 1xmf.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1xmf_validation.pdf.gz | 485.1 KB | Display | wwPDB validaton report |
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Full document | 1xmf_full_validation.pdf.gz | 545.1 KB | Display | |
Data in XML | 1xmf_validation.xml.gz | 90.8 KB | Display | |
Data in CIF | 1xmf_validation.cif.gz | 127.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xm/1xmf ftp://data.pdbj.org/pub/pdb/validation_reports/xm/1xmf | HTTPS FTP |
-Related structure data
Related structure data | 1xmgC 1xmhC 1fz1S 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 / Details: gene MMOX / Source: (natural) Methylococcus capsulatus (bacteria) / Strain: Bath References: UniProt: P22869, methane monooxygenase (soluble) #2: Protein | Mass: 45111.504 Da / Num. of mol.: 2 / Fragment: beta subunit / Source method: isolated from a natural source / Details: gene MMOY / Source: (natural) Methylococcus capsulatus (bacteria) / Strain: Bath References: UniProt: P18798, methane monooxygenase (soluble) #3: Protein | Mass: 19748.537 Da / Num. of mol.: 2 / Fragment: gamma subunit / Source method: isolated from a natural source / Details: gene MMOZ / Source: (natural) Methylococcus capsulatus (bacteria) / Strain: Bath References: UniProt: P11987, methane monooxygenase (soluble) |
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-Non-polymers , 3 types, 1121 molecules
#4: Chemical | ChemComp-MN / #5: Chemical | ChemComp-CA / #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: 2.59 Å3/Da / Density % sol: 52.2 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7 Details: MOPS, CaCl2, PEG8000, glycerol, azide, 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: BL7-1 / Wavelength: 1.08 Å |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: May 1, 2002 |
Radiation | Monochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.08 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→30 Å / Num. all: 132599 / Num. obs: 117119 / % possible obs: 91.7 % / Observed criterion σ(I): 1 / Redundancy: 2.3 % / Biso Wilson estimate: 19.1 Å2 / Rmerge(I) obs: 0.058 / Rsym value: 0.058 / Net I/σ(I): 11.3 |
Reflection shell | Resolution: 2.3→2.38 Å / Redundancy: 1.7 % / Rmerge(I) obs: 0.295 / Mean I/σ(I) obs: 2.8 / Rsym value: 0.295 / % possible all: 90.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB 1FZ1 Resolution: 2.32→28.76 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 415690.79 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 38.0333 Å2 / ksol: 0.330296 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 43.2 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.32→28.76 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.32→2.47 Å / Rfactor Rfree error: 0.015 / Total num. of bins used: 6
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Xplor file |
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