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- PDB-7cfx: NAD-soaked Holo-methanol dehydrogenase (MDH) from Methylococcus c... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7cfx | ||||||
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Title | NAD-soaked Holo-methanol dehydrogenase (MDH) from Methylococcus capsulatus (Bath) | ||||||
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Function / homology | ![]() alcohol dehydrogenase (cytochrome c(L)) activity / ![]() ![]() ![]() Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | 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 | ![]()
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![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 996.1 KB | Display | ![]() |
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PDB format | ![]() | 825.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 7cdlC ![]() 7ce5C ![]() 7ce9C ![]() 7cedC ![]() 4tqoS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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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) ![]() ![]() 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) ![]() ![]() Strain: ATCC 33009 / NCIMB 11132 / Bath References: UniProt: Q60AR3, ![]() #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: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.6 Å3/Da / Density % sol: 52.7 % |
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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: ![]() ![]() ![]() |
Detector | Type: RAYONIX MX300HE / Detector: CCD / Date: Jun 9, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 2.3→30 Å / Num. obs: 195256 / % possible obs: 99.2 % / Redundancy: 6.3 % / CC1/2: 0.85 / CC star: 0.95 / Net I/σ(I): 13.5 |
Reflection shell | Resolution: 2.3→2.4 Å / Num. unique obs: 26426 / Rpim(I) all: 0.34 / % possible all: 99 |
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Processing
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Refinement | Method to determine structure![]() ![]() Starting model: 4TQO Resolution: 2.5→30 Å / Cross valid method: THROUGHOUT
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Refinement step | Cycle: LAST / Resolution: 2.5→30 Å
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LS refinement shell | Resolution: 2.5→2.56 Å
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