[English] 日本語
Yorodumi- PDB-7ce5: Methanol-PQQ bound methanol dehydrogenase (MDH) from Methylococcu... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7ce5 | ||||||
---|---|---|---|---|---|---|---|
Title | Methanol-PQQ bound methanol dehydrogenase (MDH) from Methylococcus capsulatus (Bath) | ||||||
Components | (Methanol dehydrogenase ...) x 2 | ||||||
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: 1.8 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
| ||||||
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 |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 7ce5.cif.gz | 1.1 MB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb7ce5.ent.gz | 906.8 KB | Display | PDB format |
PDBx/mmJSON format | 7ce5.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ce/7ce5 ftp://data.pdbj.org/pub/pdb/validation_reports/ce/7ce5 | HTTPS FTP |
---|
-Related structure data
Related structure data | 7cdlC 7ce9C 7cedC 7cfxC 4tqoS C: citing same article (ref.) S: Starting model for refinement |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
2 |
| ||||||||
3 |
| ||||||||
4 |
| ||||||||
5 |
| ||||||||
6 |
| ||||||||
7 |
| ||||||||
8 |
| ||||||||
Unit cell |
|
-Components
-Methanol dehydrogenase ... , 2 types, 16 molecules ABCDGHMNEFIJKLOP
#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: obtained synthetically Source: (synth.) Methylococcus capsulatus (strain ATCC 33009 / NCIMB 11132 / Bath) (bacteria) References: UniProt: Q60AR3, methanol dehydrogenase (cytochrome c) |
---|
-Non-polymers , 4 types, 5374 molecules
#3: Chemical | ChemComp-CA / #4: Chemical | ChemComp-MOH / #5: Chemical | ChemComp-PQQ / #6: Water | ChemComp-HOH / | |
---|
-Details
Has ligand of interest | Y |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.66 Å3/Da / Density % sol: 53.67 % |
---|---|
Crystal grow | Temperature: 291.15 K / Method: microbatch / pH: 7.5 / Details: Hepes, PEG600 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
---|---|
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: 1.8→153 Å / Num. obs: 535098 / % possible obs: 99.8 % / Redundancy: 3.5 % / CC1/2: 0.9 / Net I/σ(I): 14.11 |
Reflection shell | Resolution: 1.8→1.9 Å / Num. unique obs: 176635 / CC1/2: 0.86 |
-Processing
Software |
| ||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4TQO Resolution: 1.8→153 Å / Cross valid method: THROUGHOUT
| ||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.8→153 Å
| ||||||||||||||||||||
LS refinement shell | Resolution: 1.8→1.84 Å
|