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Yorodumi- PDB-1efv: THREE-DIMENSIONAL STRUCTURE OF HUMAN ELECTRON TRANSFER FLAVOPROTE... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1efv | ||||||
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Title | THREE-DIMENSIONAL STRUCTURE OF HUMAN ELECTRON TRANSFER FLAVOPROTEIN TO 2.1 A RESOLUTION | ||||||
Components | (ELECTRON TRANSFER FLAVOPROTEINElectron-transferring flavoprotein) x 2 | ||||||
Keywords | ELECTRON TRANSPORT / FLAVOPROTEIN / GLUTARIC ACIDEMIA TYPE II | ||||||
Function / homology | Function and homology information electron transfer flavoprotein complex / fatty acid beta-oxidation using acyl-CoA dehydrogenase / amino acid catabolic process / Respiratory electron transport / Protein methylation / respiratory electron transport chain / flavin adenine dinucleotide binding / electron transfer activity / oxidoreductase activity / mitochondrial matrix / mitochondrion Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / MIR / Resolution: 2.1 Å | ||||||
Authors | Roberts, D.L. / Frerman, F.E. / Kim, J.J.P. | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 1996 Title: Three-dimensional structure of human electron transfer flavoprotein to 2.1-A resolution. Authors: Roberts, D.L. / Frerman, F.E. / Kim, J.J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1efv.cif.gz | 128 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1efv.ent.gz | 96.6 KB | Display | PDB format |
PDBx/mmJSON format | 1efv.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ef/1efv ftp://data.pdbj.org/pub/pdb/validation_reports/ef/1efv | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 33134.148 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: COFACTORS FAD 1 AND AMP 1 ARE NON-COVALENTLY BOUND / Source: (gene. exp.) Homo sapiens (human) / Cellular location: MITOCHONDRIAMitochondrion / Organ: LIVER / Plasmid: PBLUESCRIPT SK+ / Production host: Escherichia coli (E. coli) / Strain (production host): DH5ALPHA / References: UniProt: P13804 |
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#2: Protein | Mass: 27885.646 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: COFACTORS FAD 1 AND AMP 1 ARE NON-COVALENTLY BOUND / Source: (gene. exp.) Homo sapiens (human) / Cellular location: MITOCHONDRIAMitochondrion / Organ: LIVER / Plasmid: PBLUESCRIPT SK+ / Production host: Escherichia coli (E. coli) / Strain (production host): DH5ALPHA / References: UniProt: P38117 |
#3: Chemical | ChemComp-FAD / |
#4: Chemical | ChemComp-AMP / |
#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: 2.69 Å3/Da / Density % sol: 50 % | ||||||||||||||||||||||||||||||
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Crystal grow | Method: vapor diffusion, sitting drop / pH: 7 Details: THE PROTEIN WAS CRYSTALLIZED FROM 15 % PEG 1500, 50 MM HEPES, PH 7.0. EQUAL VOLUMES OF PROTEIN (15 MG/ML) AND PRECIPITANT WERE MIXED IN SITTING DROPS., vapor diffusion - sitting drop | ||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 19 ℃ / Method: vapor diffusion, sitting drop | ||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 277 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RUH2R / Wavelength: 1.5418 |
Detector | Type: RIGAKU RAXIS II / Detector: IMAGE PLATE / Date: Apr 1, 1994 / Details: COLLIMATOR |
Radiation | Monochromator: GRAPHITE(002) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→30 Å / Num. obs: 32383 / % possible obs: 96 % / Observed criterion σ(I): 0 / Redundancy: 3.7 % / Rmerge(I) obs: 0.064 / Rsym value: 0.064 / Net I/σ(I): 17 |
Reflection shell | Resolution: 2.1→2.14 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.064 / Mean I/σ(I) obs: 2.6 / Rsym value: 0.304 / % possible all: 92.4 |
Reflection | *PLUS % possible obs: 95.6 % / Num. measured all: 118435 |
Reflection shell | *PLUS % possible obs: 92.4 % / Rmerge(I) obs: 0.304 |
-Processing
Software |
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Refinement | Method to determine structure: MIR / Resolution: 2.1→8 Å / σ(F): 2
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Displacement parameters | Biso mean: 27.6 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.1→8 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.1→2.19 Å / Total num. of bins used: 8
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Xplor file |
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Software | *PLUS Name: X-PLOR / Version: 3.1 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Rfactor obs: 0.171 / Rfactor Rfree: 0.221 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor obs: 0.218 |