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Yorodumi- PDB-7ce9: PQQ-soaked Apo-methanol dehydrogenase (MDH) from Methylococcus ca... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7ce9 | ||||||
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Title | PQQ-soaked Apo-methanol dehydrogenase (MDH) from Methylococcus capsulatus (Bath) | ||||||
Components |
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Keywords | OXIDOREDUCTASE / Methanol / PQQ | ||||||
Function / homology | Function and homology information alcohol dehydrogenase (cytochrome c(L)) activity / methanol dehydrogenase (cytochrome c) / methanol oxidation / oxidoreductase activity, acting on CH-OH group of donors / alcohol dehydrogenase (NAD+) activity / outer membrane-bounded periplasmic space / calcium ion binding / membrane Similarity search - Function | ||||||
Biological species | Methylococcus capsulatus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å | ||||||
Authors | Chuankhayan, P. / Chan, S.I. / Nareddy, P.K.R. / Tsai, I.K. / Tsai, Y.F. / Chen, K.H.-C. / Yu, S.S.-F. / Chen, C.J. | ||||||
Funding support | Taiwan, 1items
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Citation | Journal: J.Am.Chem.Soc. / Year: 2021 Title: Mechanism of Pyrroloquinoline Quinone-Dependent Hydride Transfer Chemistry from Spectroscopic and High-Resolution X-ray Structural Studies of the Methanol Dehydrogenase from Methylococcus capsulatus (Bath). Authors: Chan, S.I. / Chuankhayan, P. / Reddy Nareddy, P.K. / Tsai, I.K. / Tsai, Y.F. / Chen, K.H. / Yu, S.S. / Chen, C.J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7ce9.cif.gz | 1 MB | Display | PDBx/mmCIF format |
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PDB format | pdb7ce9.ent.gz | 854.3 KB | Display | PDB format |
PDBx/mmJSON format | 7ce9.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7ce9_validation.pdf.gz | 2.8 MB | Display | wwPDB validaton report |
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Full document | 7ce9_full_validation.pdf.gz | 2.8 MB | Display | |
Data in XML | 7ce9_validation.xml.gz | 198.9 KB | Display | |
Data in CIF | 7ce9_validation.cif.gz | 283.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ce/7ce9 ftp://data.pdbj.org/pub/pdb/validation_reports/ce/7ce9 | HTTPS FTP |
-Related structure data
Related structure data | 7cdlC 7ce5C 7cedC 7cfxC 4tqoS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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2 |
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3 |
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8 |
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Unit cell |
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-Components
#1: Protein | Mass: 63688.789 Da / Num. of mol.: 8 / Source method: isolated from a natural source Source: (natural) Methylococcus capsulatus (strain ATCC 33009 / NCIMB 11132 / Bath) (bacteria) Strain: ATCC 33009 / NCIMB 11132 / Bath / References: UniProt: Q60AR6 #2: Protein | Mass: 8229.256 Da / Num. of mol.: 8 / Source method: isolated from a natural source Source: (natural) Methylococcus capsulatus (strain ATCC 33009 / NCIMB 11132 / Bath) (bacteria) Strain: ATCC 33009 / NCIMB 11132 / Bath References: UniProt: Q60AR3, methanol dehydrogenase (cytochrome c) #3: Chemical | ChemComp-CA / #4: Chemical | ChemComp-PQQ / #5: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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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: 2.65 Å3/Da / Density % sol: 53.53 % |
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Crystal grow | Temperature: 291 K / Method: microbatch / Details: Hepes, PEG600 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 0.9 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 27, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→153.79 Å / Num. obs: 292773 / % possible obs: 99.2 % / Redundancy: 3.3 % / CC1/2: 0.9 / Net I/σ(I): 11.76 |
Reflection shell | Resolution: 2.2→2.33 Å / Num. unique obs: 95297 / CC1/2: 0.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4TQO Resolution: 2.2→153 Å / Cross valid method: THROUGHOUT
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Refinement step | Cycle: LAST / Resolution: 2.2→153 Å
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LS refinement shell | Resolution: 2.2→2.25 Å
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