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Yorodumi- PDB-1mg3: MUTATION OF ALPHA PHE55 OF METHYLAMINE DEHYDROGENASE ALTERS THE R... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1mg3 | |||||||||
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Title | MUTATION OF ALPHA PHE55 OF METHYLAMINE DEHYDROGENASE ALTERS THE REORGANIZATION ENERGY AND ELECTRONIC COUPLING FOR ITS ELECTRON TRANSFER REACTION WITH AMICYANIN | |||||||||
Components |
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Keywords | OXIDOREDUCTASE / electron transfer / methylamine dehydrogenase / cytochrome / blue copper protein / active site mutant / phenylhydrazine adduct. | |||||||||
Function / homology | Function and homology information microtubule-dependent intracellular transport of viral material towards cell periphery / methanol metabolic process / methylamine dehydrogenase (amicyanin) / methylamine dehydrogenase (amicyanin) activity / methylamine metabolic process / aliphatic amine dehydrogenase activity / amine metabolic process / host cell / host cell endosome / outer membrane-bounded periplasmic space ...microtubule-dependent intracellular transport of viral material towards cell periphery / methanol metabolic process / methylamine dehydrogenase (amicyanin) / methylamine dehydrogenase (amicyanin) activity / methylamine metabolic process / aliphatic amine dehydrogenase activity / amine metabolic process / host cell / host cell endosome / outer membrane-bounded periplasmic space / periplasmic space / electron transfer activity / iron ion binding / copper ion binding / heme binding / virion membrane / membrane Similarity search - Function | |||||||||
Biological species | Paracoccus denitrificans (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / refined directly / Resolution: 2.4 Å | |||||||||
Authors | Sun, D. / Chen, Z.W. / Mathews, F.S. / Davidson, V.L. | |||||||||
Citation | Journal: Biochemistry / Year: 2002 Title: MUTATION OF ALPHA PHE55 OF METHYLAMINE DEHYDROGENASE ALTERS THE REORGANIZATION ENERGY AND ELECTRONIC COUPLING FOR ITS ELECTRON TRANSFER REACTION WITH AMICYANIN Authors: Sun, D. / Chen, Z.W. / Mathews, F.S. / Davidson, V.L. #1: Journal: Science / Year: 1994 Title: Structure of an electron transfer complex: methylamine dehydrogenase, amicyanin, and cytochrome c551i Authors: Chen, L. / Durley, R. / Mathews, F.S. / Davidson, V.L. | |||||||||
History |
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Remark 999 | SEQUENCE The authors maintain that the sequence in the sequence database is wrong. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1mg3.cif.gz | 602.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1mg3.ent.gz | 506.9 KB | Display | PDB format |
PDBx/mmJSON format | 1mg3.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1mg3_validation.pdf.gz | 1.7 MB | Display | wwPDB validaton report |
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Full document | 1mg3_full_validation.pdf.gz | 1.8 MB | Display | |
Data in XML | 1mg3_validation.xml.gz | 124.1 KB | Display | |
Data in CIF | 1mg3_validation.cif.gz | 168.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/mg/1mg3 ftp://data.pdbj.org/pub/pdb/validation_reports/mg/1mg3 | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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Details | two heterooctameric molecules per asymmetric unit |
-Components
-Protein , 2 types, 8 molecules CGKODHLP
#3: Protein | Mass: 11505.171 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Paracoccus denitrificans (bacteria) / Production host: Rhodobacter sphaeroides (bacteria) / References: UniProt: P22364 #4: Protein | Mass: 17094.650 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Paracoccus denitrificans (bacteria) / Production host: Rhodobacter sphaeroides (bacteria) / References: UniProt: P29889, UniProt: P29899*PLUS |
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-Methylamine dehydrogenase, ... / Antibody , 2 types, 8 molecules AEIMBFJN
#1: Protein | Mass: 42673.492 Da / Num. of mol.: 4 / Mutation: F55A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Paracoccus denitrificans (bacteria) / Production host: Rhodobacter sphaeroides (bacteria) / References: UniProt: P29894, EC: 1.4.99.3 #2: Antibody | Mass: 14286.839 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Paracoccus denitrificans (bacteria) / Production host: Rhodobacter sphaeroides (bacteria) / References: UniProt: P22619, EC: 1.4.99.3 |
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-Non-polymers , 5 types, 862 molecules
#5: Chemical | ChemComp-PO4 / #6: Chemical | ChemComp-CU / #7: Chemical | ChemComp-NA / #8: Chemical | ChemComp-HEC / #9: 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: 2.75 Å3/Da / Density % sol: 55.31 % | ||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, sitting drop / pH: 5 Details: phosphate, pH 5.0, VAPOR DIFFUSION, SITTING DROP, temperature 295K | ||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS | ||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å |
Detector | Type: RIGAKU RAXIS IIC / Detector: IMAGE PLATE / Date: Oct 12, 2001 |
Radiation | Monochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.4→50 Å / Num. all: 144988 / Num. obs: 117875 / % possible obs: 81.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.7 % / Biso Wilson estimate: 8.7 Å2 / Rmerge(I) obs: 0.093 / Net I/σ(I): 9.3 |
Reflection shell | Resolution: 2.4→2.49 Å / Redundancy: 2 % / Rmerge(I) obs: 0.246 / Mean I/σ(I) obs: 2.2 / Num. unique all: 7336 / % possible all: 50.7 |
Reflection shell | *PLUS Lowest resolution: 2.45 Å / % possible obs: 50.7 % |
-Processing
Software |
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Refinement | Method to determine structure: refined directly Starting model: mutant complex structure Resolution: 2.4→50 Å / Rfactor Rfree error: 0.002 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Bsol: 31.6182 Å2 / ksol: 0.364008 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 30.7 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.4→50 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 6
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Refinement | *PLUS % reflection Rfree: 10 % | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Highest resolution: 2.4 Å / Lowest resolution: 2.45 Å / Rfactor Rfree: 0.397 / Rfactor Rwork: 0.377 |