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Yorodumi- PDB-1mty: METHANE MONOOXYGENASE HYDROXYLASE FROM METHYLOCOCCUS CAPSULATUS (BATH) -
+Open data
-Basic information
Entry | Database: PDB / ID: 1mty | ||||||
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Title | METHANE MONOOXYGENASE HYDROXYLASE FROM METHYLOCOCCUS CAPSULATUS (BATH) | ||||||
Components | (METHANE MONOOXYGENASE HYDROXYLASE) x 3 | ||||||
Keywords | MONOOXYGENASE / METHANE MONOOXYGENASE / HYDROXYLASE / 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 str. Bath (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å | ||||||
Authors | Rosenzweig, A.C. / Nordlund, P. / Lippard, S.J. / Frederick, C.A. | ||||||
Citation | Journal: Proteins / Year: 1997 Title: Crystal structures of the methane monooxygenase hydroxylase from Methylococcus capsulatus (Bath): implications for substrate gating and component interactions. Authors: Rosenzweig, A.C. / Brandstetter, H. / Whittington, D.A. / Nordlund, P. / Lippard, S.J. / Frederick, C.A. #1: Journal: Chem.Biol. / Year: 1995 Title: Geometry of the Soluble Methane Monooxygenase Catalytic Diiron Center in Two Oxidation States Authors: Rosenzweig, A.C. / Nordlund, P. / Takahara, P.M. / 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 | 1mty.cif.gz | 582.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1mty.ent.gz | 477.4 KB | Display | PDB format |
PDBx/mmJSON format | 1mty.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1mty_validation.pdf.gz | 405.5 KB | Display | wwPDB validaton report |
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Full document | 1mty_full_validation.pdf.gz | 457.2 KB | Display | |
Data in XML | 1mty_validation.xml.gz | 45.8 KB | Display | |
Data in CIF | 1mty_validation.cif.gz | 76.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/mt/1mty ftp://data.pdbj.org/pub/pdb/validation_reports/mt/1mty | HTTPS FTP |
-Related structure data
Related structure data | 1mmoS 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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Noncrystallographic symmetry (NCS) | NCS oper: (Code: given Matrix: (-0.999971, 0.007615, 4.2E-5), Vector: |
-Components
#1: Protein | Mass: 59241.492 Da / Num. of mol.: 2 / Source method: isolated from a natural source Source: (natural) Methylococcus capsulatus str. Bath (bacteria) Cellular location: CYTOPLASM / Species: Methylococcus capsulatus / Strain: BATH References: UniProt: P22869, methane monooxygenase (soluble) #2: Protein | Mass: 44664.988 Da / Num. of mol.: 2 / Source method: isolated from a natural source Source: (natural) Methylococcus capsulatus str. Bath (bacteria) Cellular location: CYTOPLASM / Species: Methylococcus capsulatus / Strain: BATH References: UniProt: P18798, methane monooxygenase (soluble) #3: Protein | Mass: 18980.639 Da / Num. of mol.: 2 / Source method: isolated from a natural source Source: (natural) Methylococcus capsulatus str. Bath (bacteria) Cellular location: CYTOPLASM / Species: Methylococcus capsulatus / Strain: BATH References: UniProt: P11987, methane monooxygenase (soluble) #4: Chemical | ChemComp-FE / #5: 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: 2.2 Å3/Da / Density % sol: 44 % Description: DATA WERE COLLECTED USING THE WEISSENBERG METHOD. | ||||||||||||||||||||||||||||||
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Crystal grow | pH: 7 Details: 25 MM LI2SO4, 50 MM NH4OAC, 5% PEG 4000, IN 25 MM MOPS PH 7.0 WITH A RESERVOIR OF 20% PEG 4000 | ||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 4 ℃ / Method: vapor diffusion, hanging drop / Details: macroseeding | ||||||||||||||||||||||||||||||
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: Photon Factory / Beamline: BL-6A / Wavelength: 0.9 |
Detector | Type: FUJI / Detector: IMAGE PLATE / Date: Dec 1, 1994 |
Radiation | Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→12 Å / Num. obs: 188161 / % possible obs: 77 % / Observed criterion σ(I): 0 / Redundancy: 2.5 % / Biso Wilson estimate: 13.2 Å2 / Rmerge(I) obs: 0.039 / Rsym value: 0.039 / Net I/σ(I): 20 |
Reflection shell | Resolution: 1.7→1.73 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.237 / Mean I/σ(I) obs: 20 / Rsym value: 0.237 / % possible all: 75 |
Reflection shell | *PLUS % possible obs: 75 % |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1MMO Resolution: 1.7→5 Å / σ(F): 0
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Displacement parameters | Biso mean: 9.1 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze | Luzzati coordinate error obs: 0.2 Å / Luzzati d res low obs: 5 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.7→5 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.7→1.73 Å
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Xplor file |
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Software | *PLUS Name: X-PLOR / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor obs: 0.245 |