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Yorodumi- PDB-3sws: Crystal Structure of the Quinone Form of Methylamine Dehydrogenas... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3sws | ||||||
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Title | Crystal Structure of the Quinone Form of Methylamine Dehydrogenase in Complex with the Diferric Form of MauG | ||||||
Components |
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Keywords | OXIDOREDUCTASE/ELECTRON TRANSPORT / MauG / methylamine dehydrogenase / TTQ / c-heme / OXIDOREDUCTASE-ELECTRON TRANSPORT complex | ||||||
Function / homology | Function and homology information methylamine dehydrogenase (amicyanin) / methylamine dehydrogenase (amicyanin) activity / methylamine metabolic process / aliphatic amine dehydrogenase activity / amine metabolic process / Oxidoreductases / cytochrome-c peroxidase activity / outer membrane-bounded periplasmic space / periplasmic space / electron transfer activity ...methylamine dehydrogenase (amicyanin) / methylamine dehydrogenase (amicyanin) activity / methylamine metabolic process / aliphatic amine dehydrogenase activity / amine metabolic process / Oxidoreductases / cytochrome-c peroxidase activity / outer membrane-bounded periplasmic space / periplasmic space / electron transfer activity / heme binding / metal ion binding Similarity search - Function | ||||||
Biological species | Paracoccus denitrificans (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.86 Å | ||||||
Authors | Jensen, L.M.R. / Wilmot, C.M. | ||||||
Citation | Journal: To be Published Title: Crystal Structure of the Quinone Form of Methylamine Dehydrogenase in Complex with the Diferric Form of MauG Authors: Jensen, L.M.R. / Wilmot, C.M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3sws.cif.gz | 713.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3sws.ent.gz | 580.7 KB | Display | PDB format |
PDBx/mmJSON format | 3sws.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3sws_validation.pdf.gz | 1.9 MB | Display | wwPDB validaton report |
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Full document | 3sws_full_validation.pdf.gz | 1.9 MB | Display | |
Data in XML | 3sws_validation.xml.gz | 86 KB | Display | |
Data in CIF | 3sws_validation.cif.gz | 128.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/sw/3sws ftp://data.pdbj.org/pub/pdb/validation_reports/sw/3sws | HTTPS FTP |
-Related structure data
Related structure data | 3l4mS 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
-Protein / Antibody / Methylamine dehydrogenase ... , 3 types, 6 molecules ABCEDF
#1: Protein | Mass: 41146.629 Da / Num. of mol.: 2 / Fragment: UNP residues 21-387 Source method: isolated from a genetically manipulated source Details: WT-MauG produced / Source: (gene. exp.) Paracoccus denitrificans (bacteria) / Strain: Pd 1222 / Gene: mauG, Pden_4736 / Production host: Paracoccus denitrificans (bacteria) / References: UniProt: Q51658, Oxidoreductases #2: Antibody | Mass: 15039.577 Da / Num. of mol.: 2 / Fragment: UNP residues 58-188 Source method: isolated from a genetically manipulated source Details: Mature MADH produced / Source: (gene. exp.) Paracoccus denitrificans (bacteria) / Strain: Pd 1222 / Gene: mauA / Production host: Rhodobacter sphaeroides (bacteria) References: UniProt: P22619, UniProt: A1BBA0*PLUS, EC: 1.4.99.3 #3: Protein | Mass: 42449.277 Da / Num. of mol.: 2 / Fragment: UNP residues 32-417 Source method: isolated from a genetically manipulated source Details: Mature MADH produced / Source: (gene. exp.) Paracoccus denitrificans (bacteria) / Strain: Pd 1222 / Gene: Pden_4730 / Production host: Rhodobacter sphaeroides (bacteria) / References: UniProt: A1BB97, EC: 1.4.99.3 |
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-Non-polymers , 9 types, 2026 molecules
#4: Chemical | #5: Chemical | ChemComp-NA / #6: Chemical | ChemComp-HEC / #7: Chemical | #8: Chemical | ChemComp-MES / | #9: Chemical | ChemComp-ACT / | #10: Chemical | ChemComp-1PE / | #11: Chemical | ChemComp-PG4 / | #12: 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: 2.46 Å3/Da / Density % sol: 50.07 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.2 Details: Drops contained 1uL protein with 3uL reservoir solution. Protein solution: 100uM WT-MauG and 50uM MADH in 10mM potassium phosphate pH 7.5. Reservoir solution contained: 25% w/v PEG 8000, 0. ...Details: Drops contained 1uL protein with 3uL reservoir solution. Protein solution: 100uM WT-MauG and 50uM MADH in 10mM potassium phosphate pH 7.5. Reservoir solution contained: 25% w/v PEG 8000, 0.1M sodium acetate, 0.1M MES pH 6.2., VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.03322 Å |
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jun 26, 2010 / Details: Biomorph mirrors (Kirkpatrick-Baez configuration) |
Radiation | Monochromator: Si(111) double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.03322 Å / Relative weight: 1 |
Reflection | Resolution: 1.86→50 Å / Num. all: 158031 / Num. obs: 154080 / % possible obs: 97.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 3.8 % / Rsym value: 0.097 / Net I/σ(I): 13.9 |
Reflection shell | Resolution: 1.86→1.89 Å / Redundancy: 3.7 % / Mean I/σ(I) obs: 3 / Num. unique all: 7900 / Rsym value: 0.472 / % possible all: 95.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3L4M Resolution: 1.86→49.12 Å / Cor.coef. Fo:Fc: 0.973 / Cor.coef. Fo:Fc free: 0.955 / SU B: 5.126 / SU ML: 0.07 / Cross valid method: THROUGHOUT / ESU R Free: 0.111 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 21.476 Å2
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Refinement step | Cycle: LAST / Resolution: 1.86→49.12 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.86→1.907 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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