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- PDB-7cdl: holo-methanol dehydrogenase (MDH) with Cys131-Cys132 reduced from... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7cdl | ||||||
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Title | holo-methanol dehydrogenase (MDH) with Cys131-Cys132 reduced 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. | ||||||
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 1.1 MB | Display | ![]() |
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PDB format | ![]() | 892.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 7ce5C ![]() 7ce9C ![]() 7cedC ![]() 7cfxC ![]() 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 Details: The sample sequence in the entity_poly section of the coordinate CIF file includes all residues used in the experiment and final-residue missing due to disorder. 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: 2.62 Å3/Da / Density % sol: 52.97 % |
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Crystal grow![]() | Temperature: 291.15 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: Apr 10, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 1.85→30 Å / Num. obs: 508926 / % possible obs: 99.82 % / Redundancy: 7.4 % / CC1/2: 0.814 / Net I/σ(I): 2.42 |
Reflection shell | Resolution: 1.85→1.92 Å / Redundancy: 7.2 % / Num. unique obs: 50612 / CC1/2: 0.804 / % possible all: 100 |
-Phasing
Phasing![]() | Method: ![]() |
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Processing
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Refinement | Method to determine structure![]() ![]() Starting model: 4TQO Resolution: 1.85→30 Å / Cross valid method: THROUGHOUT
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Displacement parameters | Biso mean: 23 Å2 | ||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.85→30 Å
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LS refinement shell | Resolution: 1.85→1.91 Å
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