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Yorodumi- PDB-1o97: Structure of electron transferring flavoprotein from Methylophilu... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1o97 | ||||||
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Title | Structure of electron transferring flavoprotein from Methylophilus methylotrophus, recognition loop removed by limited proteolysis | ||||||
Components |
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Keywords | ELECTRON TRANSFER / FLAVOPROTEIN / FAD BINDING | ||||||
Function / homology | Function and homology information fatty acid beta-oxidation using acyl-CoA dehydrogenase / amino acid catabolic process / flavin adenine dinucleotide binding / electron transfer activity / nucleotide binding / cytosol Similarity search - Function | ||||||
Biological species | METHYLOPHILUS METHYLOTROPHUS (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 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 |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1o97.cif.gz | 137.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1o97.ent.gz | 105.6 KB | Display | PDB format |
PDBx/mmJSON format | 1o97.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1o97_validation.pdf.gz | 1 MB | Display | wwPDB validaton report |
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Full document | 1o97_full_validation.pdf.gz | 1 MB | Display | |
Data in XML | 1o97_validation.xml.gz | 31.8 KB | Display | |
Data in CIF | 1o97_validation.cif.gz | 47.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/o9/1o97 ftp://data.pdbj.org/pub/pdb/validation_reports/o9/1o97 | HTTPS FTP |
-Related 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: 28929.850 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) METHYLOPHILUS METHYLOTROPHUS (bacteria) Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P53570 |
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#2: Protein | Mass: 33622.945 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) METHYLOPHILUS METHYLOTROPHUS (bacteria) Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P53571 |
#3: Chemical | ChemComp-AMP / |
#4: Chemical | ChemComp-FAD / |
#5: Water | ChemComp-HOH / |
-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: 55.26 % | ||||||||||||||||||||||||
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Crystal grow | pH: 6.5 / Details: 2.5 M POTASSIUM PHOSPHATE PH 6.3 | ||||||||||||||||||||||||
Crystal grow | *PLUS Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 1 |
Detector | Date: May 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: 1.6→20 Å / Num. obs: 85935 / % possible obs: 96.3 % / Redundancy: 5.2 % / Rmerge(I) obs: 0.069 / Net I/σ(I): 16.1 |
Reflection shell | Resolution: 1.6→1.65 Å / Redundancy: 4.9 % / Rmerge(I) obs: 0.28 / Mean I/σ(I) obs: 2.7 / % possible all: 95.5 |
Reflection | *PLUS Lowest resolution: 20 Å / Num. measured all: 876371 |
Reflection shell | *PLUS Highest resolution: 1.6 Å / Lowest resolution: 1.63 Å / % possible obs: 95.5 % / Rmerge(I) obs: 0.285 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.6→19.92 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.95 / SU B: 1.914 / SU ML: 0.067 / Cross valid method: THROUGHOUT / ESU R: 0.093 / ESU R Free: 0.092 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: DISORDERED REGIONS AND SIDECHAINS WERE NOT INCLUDED IN THE MODEL.
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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: 25.11 Å2
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Refinement step | Cycle: LAST / Resolution: 1.6→19.92 Å
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Refine LS restraints |
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