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Yorodumi- PDB-5xm3: Crystal Structure of Methanol dehydrogenase from Methylophaga ami... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5xm3 | ||||||
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Title | Crystal Structure of Methanol dehydrogenase from Methylophaga aminisulfidivorans | ||||||
Components |
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Keywords | OXIDOREDUCTASE / marine / methanol dehydrogenase / methylophaga / pyrroloquinoline quinone / Mg++ | ||||||
Function / homology | Function and homology information alcohol dehydrogenase (cytochrome c(L)) activity => GO:0052933 / alcohol dehydrogenase (cytochrome c(L)) activity => GO:0052933 / alcohol dehydrogenase (cytochrome c(L)) activity => GO:0052933 / 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 | Methylophaga aminisulfidivorans MP (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.701 Å | ||||||
Authors | Cao, T.P. / Choi, J.M. / Lee, S.H. | ||||||
Funding support | Korea, Republic Of, 1items
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Citation | Journal: J. Microbiol. / Year: 2018 Title: The crystal structure of methanol dehydrogenase, a quinoprotein from the marine methylotrophic bacterium Methylophaga aminisulfidivorans MPT Authors: Cao, T.P. / Choi, J.M. / Kim, S.W. / Lee, S.H. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5xm3.cif.gz | 555.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5xm3.ent.gz | 452.5 KB | Display | PDB format |
PDBx/mmJSON format | 5xm3.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5xm3_validation.pdf.gz | 1.2 MB | Display | wwPDB validaton report |
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Full document | 5xm3_full_validation.pdf.gz | 1.2 MB | Display | |
Data in XML | 5xm3_validation.xml.gz | 54.1 KB | Display | |
Data in CIF | 5xm3_validation.cif.gz | 80.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xm/5xm3 ftp://data.pdbj.org/pub/pdb/validation_reports/xm/5xm3 | HTTPS FTP |
-Related structure data
Related structure data | 1w6sS 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: 69341.836 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Methylophaga aminisulfidivorans MP (bacteria) Gene: MAMP_01209 Production host: Methylophaga aminisulfidivorans MP (bacteria) References: UniProt: A3FJ48 #2: Protein | Mass: 9978.702 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Methylophaga aminisulfidivorans MP (bacteria) Gene: MAMP_01202 Production host: Methylophaga aminisulfidivorans MP (bacteria) References: UniProt: A3FJ51, methanol dehydrogenase (cytochrome c) #3: Chemical | #4: Chemical | #5: Water | ChemComp-HOH / | |
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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: 2.12 Å3/Da / Density % sol: 41.89 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 0.1M sodium cacodylate pH 6.5, 0.2M magnesium acetate tetrahydrate, 10%(v/v) PEG 8000 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: PAL/PLS / Beamline: 5C (4A) / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 21, 2009 |
Radiation | Monochromator: DCM Si (111) Crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→50 Å / Num. obs: 140904 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 5.3 % / Rmerge(I) obs: 0.112 / Net I/σ(I): 24.55 |
Reflection shell | Resolution: 1.7→1.73 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.478 / Mean I/σ(I) obs: 2.827 / Num. unique obs: 6897 / % possible all: 98.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1W6S Resolution: 1.701→34.724 Å / SU ML: 0.16 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 17.12 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.701→34.724 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: 8.8433 Å / Origin y: -1.0738 Å / Origin z: 27.8722 Å
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Refinement TLS group | Selection details: all |