[English] 日本語
Yorodumi- PDB-1o94: Ternary complex between trimethylamine dehydrogenase and electron... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1o94 | ||||||
---|---|---|---|---|---|---|---|
Title | Ternary complex between trimethylamine dehydrogenase and electron transferring flavoprotein | ||||||
Components |
| ||||||
Keywords | ELECTRON TRANSPORT / PROTEIN COMPLEX / ELECTRON TRANSFER / DEHYDROGENASE | ||||||
Function / homology | Function and homology information trimethylamine dehydrogenase / trimethylamine dehydrogenase activity / fatty acid beta-oxidation, unsaturated, even number, reductase/isomerase pathway / 2,4-dienoyl-CoA reductase (NADPH) activity / fatty acid beta-oxidation using acyl-CoA dehydrogenase / amino acid catabolic process / FMN binding / flavin adenine dinucleotide binding / 4 iron, 4 sulfur cluster binding / electron transfer activity ...trimethylamine dehydrogenase / trimethylamine dehydrogenase activity / fatty acid beta-oxidation, unsaturated, even number, reductase/isomerase pathway / 2,4-dienoyl-CoA reductase (NADPH) activity / fatty acid beta-oxidation using acyl-CoA dehydrogenase / amino acid catabolic process / FMN binding / flavin adenine dinucleotide binding / 4 iron, 4 sulfur cluster binding / electron transfer activity / nucleotide binding / metal ion binding / cytosol Similarity search - Function | ||||||
Biological species | METHYLOPHILUS METHYLOTROPHUS (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å | ||||||
Authors | Leys, D. / Basran, J. / Talfournier, F. / Sutcliffe, M.J. / Scrutton, N.S. | ||||||
Citation | Journal: Nat.Struct.Biol. / Year: 2003 Title: Extensive Conformational Sampling in a Ternary Electron Transfer Complex. Authors: Leys, D. / Basran, J. / Talfournier, F. / Sutcliffe, M.J. / Scrutton, N.S. | ||||||
History |
| ||||||
Remark 700 | SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 1o94.cif.gz | 501.5 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb1o94.ent.gz | 402 KB | Display | PDB format |
PDBx/mmJSON format | 1o94.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1o94_validation.pdf.gz | 2.3 MB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 1o94_full_validation.pdf.gz | 2.3 MB | Display | |
Data in XML | 1o94_validation.xml.gz | 107.5 KB | Display | |
Data in CIF | 1o94_validation.cif.gz | 158.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/o9/1o94 ftp://data.pdbj.org/pub/pdb/validation_reports/o9/1o94 | HTTPS FTP |
-Related structure data
Related structure data | 1o95C 1o96C 1o97C 2tmdS C: citing same article (ref.) S: Starting model for refinement |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
| ||||||||
Components on special symmetry positions |
|
-Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 81606.023 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: LINK BETWEEN FMN AND RESIDUE 30 / Source: (natural) METHYLOPHILUS METHYLOTROPHUS (bacteria) / References: UniProt: P16099, EC: 1.5.99.7 |
---|
-ELECTRON TRANSFER FLAVOPROTEIN ... , 2 types, 4 molecules CEDF
#2: Protein | Mass: 28929.850 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) METHYLOPHILUS METHYLOTROPHUS (bacteria) Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P53570 #3: Protein | Mass: 33622.945 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) METHYLOPHILUS METHYLOTROPHUS (bacteria) Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P53571 |
---|
-Non-polymers , 5 types, 2157 molecules
#4: Chemical | #5: Chemical | #6: Chemical | #7: Chemical | #8: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.71 Å3/Da / Density % sol: 54.55 % | ||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Crystal grow | pH: 6.5 Details: 8% PEG 20000, 8% PEG 750 MME, 0.1-0.3 M SODIUM ACETATE, pH 6.50 | ||||||||||||||||||||||||
Crystal grow | *PLUS Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||
Components of the solutions | *PLUS
|
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: SRS / Beamline: PX9.6 / Wavelength: 1 |
Detector | Detector: CCD / Date: Apr 15, 2002 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2→20 Å / Num. obs: 184949 / % possible obs: 94.8 % / Redundancy: 3.2 % / Rmerge(I) obs: 0.071 / Net I/σ(I): 11.5 |
Reflection shell | Resolution: 2→2.05 Å / Rmerge(I) obs: 0.251 / Mean I/σ(I) obs: 2.9 / % possible all: 89.5 |
Reflection | *PLUS Lowest resolution: 20 Å / Num. obs: 184250 / Num. measured all: 1099561 |
Reflection shell | *PLUS Highest resolution: 2 Å / Lowest resolution: 2.07 Å / % possible obs: 89.5 % |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2TMD Resolution: 2→19.88 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.946 / SU B: 3.369 / SU ML: 0.094 / Cross valid method: THROUGHOUT / ESU R: 0.152 / ESU R Free: 0.141 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: DISORDERED REGIONS ARE NOT INCLUDED IN THE COORDINATES. THE ENTIRE FAD DOMAIN OF THE ETF MOLECULES IS NOT VISIBLE IN THE ELECTRON DENSITY.
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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: 33.33 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2→19.88 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
|