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Yorodumi- PDB-1djq: STRUCTURAL AND BIOCHEMICAL CHARACTERIZATION OF RECOMBINANT C30A M... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1djq | ||||||
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Title | STRUCTURAL AND BIOCHEMICAL CHARACTERIZATION OF RECOMBINANT C30A MUTANT OF TRIMETHYLAMINE DEHYDROGENASE FROM METHYLOPHILUS METHYLOTROPHUS (SP. W3A1) | ||||||
Components | TRIMETHYLAMINE DEHYDROGENASE | ||||||
Keywords | OXIDOREDUCTASE / IRON-SULFUR FLAVOPROTEIN / ELECTRON TRANSFER | ||||||
Function / homology | Function and homology information trimethylamine dehydrogenase / trimethylamine dehydrogenase activity / FMN binding / 4 iron, 4 sulfur cluster binding / metal ion binding Similarity search - Function | ||||||
Biological species | Methylophilus methylotrophus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / Resolution: 2.2 Å | ||||||
Authors | Trickey, P. / Basran, J. / Lian, L.-Y. / Chen, Z.-W. / Barton, J.D. / Sutcliffe, M.J. / Scrutton, N.S. / Mathews, F.S. | ||||||
Citation | Journal: Biochemistry / Year: 2000 Title: Structural and biochemical characterization of recombinant wild type and a C30A mutant of trimethylamine dehydrogenase from methylophilus methylotrophus (sp. W(3)A(1)). Authors: Trickey, P. / Basran, J. / Lian, L.Y. / Chen, Z. / Barton, J.D. / Sutcliffe, M.J. / Scrutton, N.S. / Mathews, F.S. #1: Journal: J.Biol.Chem. / Year: 1992 Title: Correlation of X-Ray Deduced and Experimental Amino Acid Sequences of Trimethylamine Dehydrogenase Authors: Barber, M.J. / Neame, P.J. / Lim, L.W. / White, S. / Mathews, F.S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1djq.cif.gz | 309.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1djq.ent.gz | 247.8 KB | Display | PDB format |
PDBx/mmJSON format | 1djq.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dj/1djq ftp://data.pdbj.org/pub/pdb/validation_reports/dj/1djq | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Details | The biological assembly is a dimer related by a molecular 2-fold axis. |
-Components
#1: Protein | Mass: 81573.961 Da / Num. of mol.: 2 / Mutation: C30A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Methylophilus methylotrophus (bacteria) Strain: W3A1 / Plasmid: PKK223-3 / Production host: Escherichia coli (E. coli) / Strain (production host): M13MP18 / References: UniProt: P16099, EC: 1.5.99.7 #2: Chemical | #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: 2.71 Å3/Da / Density % sol: 54.62 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop, microseeding / pH: 6.5 Details: PEG 8000, phosphate buffer, sodium chloride, pH 6.5, vapor diffusion,hanging drop and microseeding, temperature 295.0K |
Crystal grow | *PLUS Method: vapor diffusion, hanging drop |
-Data collection
Diffraction | Mean temperature: 298 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 |
Detector | Type: XUONG-HAMLIN MULTIWIRE / Detector: AREA DETECTOR / Date: Nov 21, 1995 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.22→10 Å / Num. all: 86826 / Num. obs: 81611 / % possible obs: 93.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4 % / Biso Wilson estimate: 18.6 Å2 / Rmerge(I) obs: 0.055 / Net I/σ(I): 22.2 |
Reflection shell | Resolution: 2.22→2.32 Å / Redundancy: 2.4 % / Rmerge(I) obs: 0.123 / Num. unique all: 17184 / % possible all: 71.7 |
Reflection | *PLUS Lowest resolution: 50 Å |
Reflection shell | *PLUS % possible obs: 71.7 % / Mean I/σ(I) obs: 6.4 |
-Processing
Software |
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Refinement | Resolution: 2.2→8 Å / σ(F): 2 / Stereochemistry target values: Engh & Huber
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Refinement step | Cycle: LAST / Resolution: 2.2→8 Å
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Refine LS restraints |
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