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Yorodumi- PDB-6cxh: Crystal structure of particulate methane monooxygenase from Methy... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6cxh | |||||||||
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Title | Crystal structure of particulate methane monooxygenase from Methylomicrobium alcaliphilum 20Z | |||||||||
Components |
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Keywords | OXIDOREDUCTASE / copper dependent methane monooxygenase | |||||||||
Function / homology | Function and homology information | |||||||||
Biological species | Methylomicrobium alcaliphilum 20Z (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.704 Å | |||||||||
Authors | Ro, S.Y. / Rosenzweig, A.C. | |||||||||
Funding support | United States, 2items
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Citation | Journal: J. Biol. Chem. / Year: 2018 Title: From micelles to bicelles: Effect of the membrane on particulate methane monooxygenase activity. Authors: Ro, S.Y. / Ross, M.O. / Deng, Y.W. / Batelu, S. / Lawton, T.J. / Hurley, J.D. / Stemmler, T.L. / Hoffman, B.M. / Rosenzweig, A.C. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6cxh.cif.gz | 295 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6cxh.ent.gz | 239.6 KB | Display | PDB format |
PDBx/mmJSON format | 6cxh.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6cxh_validation.pdf.gz | 835.9 KB | Display | wwPDB validaton report |
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Full document | 6cxh_full_validation.pdf.gz | 858.8 KB | Display | |
Data in XML | 6cxh_validation.xml.gz | 29.2 KB | Display | |
Data in CIF | 6cxh_validation.cif.gz | 39.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/cx/6cxh ftp://data.pdbj.org/pub/pdb/validation_reports/cx/6cxh | HTTPS FTP |
-Related structure data
Related structure data | 3rgbS 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
#1: Protein | Mass: 45602.125 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Methylomicrobium alcaliphilum 20Z (bacteria) Strain: DSM 19304 / NCIMB 14124 / VKM B-2133 / 20Z References: UniProt: G4SZ64, methane monooxygenase (soluble) |
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#2: Protein | Mass: 28277.934 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Methylomicrobium alcaliphilum 20Z (bacteria) Strain: DSM 19304 / NCIMB 14124 / VKM B-2133 / 20Z References: UniProt: G4SZ63, methane monooxygenase (soluble) |
#3: Protein | Mass: 28874.301 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Methylomicrobium alcaliphilum 20Z (bacteria) Strain: DSM 19304 / NCIMB 14124 / VKM B-2133 / 20Z References: UniProt: G4SZ62, methane monooxygenase (soluble) |
#4: Chemical | ChemComp-CU / |
#5: Chemical |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 4.25 Å3/Da / Density % sol: 71.04 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / Details: 2.8 M AmSO4, 0.2 M MES, pH 6 |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 1.033288, 1.377602 | |||||||||
Detector | Type: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Jul 28, 2016 | |||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||
Radiation wavelength |
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Reflection | Resolution: 2.7→40 Å / Num. obs: 46989 / % possible obs: 99.1 % / Redundancy: 9 % / CC1/2: 0.999 / Rpim(I) all: 0.025 / Rrim(I) all: 0.07 / Net I/σ(I): 40.6 | |||||||||
Reflection shell | Resolution: 2.7→2.8 Å / Redundancy: 6.4 % / Mean I/σ(I) obs: 11.2 / CC1/2: 0.984 / Rpim(I) all: 0.22 / Rrim(I) all: 0.588 / % possible all: 92 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3RGB Resolution: 2.704→39.579 Å / SU ML: 0.31 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 29.27
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.704→39.579 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Origin x: -168.5951 Å / Origin y: -171.7598 Å / Origin z: 8.9381 Å
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Refinement TLS group | Selection details: all |