+Open data
-Basic information
Entry | Database: PDB / ID: 1fft | ||||||
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Title | The structure of ubiquinol oxidase from Escherichia coli | ||||||
Components | (UBIQUINOL OXIDASE) x 4 | ||||||
Keywords | OXIDOREDUCTASE / ELECTRON TRANSPORT / CYTOCHROME OXIDASE / MEMBRANE PROTEIN | ||||||
Function / homology | Function and homology information cytochrome o ubiquinol oxidase complex / oxidoreduction-driven active transmembrane transporter activity / ubiquinol oxidase (H+-transporting) / cytochrome bo3 ubiquinol oxidase activity / aerobic electron transport chain / oxidoreductase activity, acting on diphenols and related substances as donors, oxygen as acceptor / cytochrome-c oxidase activity / proton transmembrane transporter activity / ubiquinone binding / electron transport coupled proton transport ...cytochrome o ubiquinol oxidase complex / oxidoreduction-driven active transmembrane transporter activity / ubiquinol oxidase (H+-transporting) / cytochrome bo3 ubiquinol oxidase activity / aerobic electron transport chain / oxidoreductase activity, acting on diphenols and related substances as donors, oxygen as acceptor / cytochrome-c oxidase activity / proton transmembrane transporter activity / ubiquinone binding / electron transport coupled proton transport / : / ATP synthesis coupled electron transport / respiratory electron transport chain / aerobic respiration / electron transfer activity / copper ion binding / heme binding / plasma membrane Similarity search - Function | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 3.5 Å | ||||||
Authors | Abramson, J. / Riistama, S. / Larsson, G. / Jasaitis, A. / Svensson-Ek, M. / Puustinen, A. / Iwata, S. / Wikstrom, M. | ||||||
Citation | Journal: Nat.Struct.Biol. / Year: 2000 Title: The structure of the ubiquinol oxidase from Escherichia coli and its ubiquinone binding site. Authors: Abramson, J. / Riistama, S. / Larsson, G. / Jasaitis, A. / Svensson-Ek, M. / Laakkonen, L. / Puustinen, A. / Iwata, S. / Wikstrom, M. #1: Journal: Acta Crystallogr.,Sect.D / Year: 2000 Title: Purification, crystallization and preliminary crystallographic studies on an integral membrane protein, cytochrome bo3 ubiquinol oxidase from Escherichia coli. Authors: Abramson, J. / Larsson, G. / Byrne, B. / Puustinen, A. / Garcia-Horsman, A. / Iwata, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1fft.cif.gz | 371.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1fft.ent.gz | 283.4 KB | Display | PDB format |
PDBx/mmJSON format | 1fft.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1fft_validation.pdf.gz | 715.6 KB | Display | wwPDB validaton report |
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Full document | 1fft_full_validation.pdf.gz | 933.4 KB | Display | |
Data in XML | 1fft_validation.xml.gz | 70.4 KB | Display | |
Data in CIF | 1fft_validation.cif.gz | 102 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ff/1fft ftp://data.pdbj.org/pub/pdb/validation_reports/ff/1fft | HTTPS FTP |
-Related structure data
Similar structure data |
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-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 | The biological assembly is a monomer composed of chains A, B, C, D, and E. |
-Components
-Protein , 4 types, 8 molecules AFBGCHDI
#1: Protein | Mass: 74424.469 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Plasmid: PBR322 / Production host: Escherichia coli (E. coli) References: UniProt: P0ABI8, Oxidoreductases; Acting on diphenols and related substances as donors; With oxygen as acceptor #2: Protein | Mass: 34947.203 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Plasmid: PBR322 / Production host: Escherichia coli (E. coli) References: UniProt: P0ABJ1, Oxidoreductases; Acting on diphenols and related substances as donors; With oxygen as acceptor #3: Protein | Mass: 22642.566 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Plasmid: PBR322 / Production host: Escherichia coli (E. coli) References: UniProt: P0ABJ3, Oxidoreductases; Acting on diphenols and related substances as donors; With oxygen as acceptor #4: Protein | Mass: 9294.448 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Plasmid: PBR322 / Production host: Escherichia coli (E. coli) References: Oxidoreductases; Acting on diphenols and related substances as donors; With oxygen as acceptor |
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-Non-polymers , 3 types, 6 molecules
#5: Chemical | #6: Chemical | #7: Chemical | |
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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: 3.53 Å3/Da / Density % sol: 65.17 % | ||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 9-10% PEG 1500, 100 mM NaCl, 100 mM MgCl2, 5% ethanol & 100 mM HEPES , pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 4K | ||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS pH: 7.5 | ||||||||||||||||||||||||||||||||||||||||||||||||
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: ID14-3 / Wavelength: 0.95 |
Detector | Type: MAR CCD 165 mm / Detector: CCD / Date: Apr 11, 1998 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.95 Å / Relative weight: 1 |
Reflection | Resolution: 3.5→40 Å / Num. obs: 44359 / % possible obs: 87 % / Observed criterion σ(I): -0.2 / Redundancy: 3.2 % / Biso Wilson estimate: 37.1 Å2 / Rmerge(I) obs: 0.123 / Net I/σ(I): 7.86 |
Reflection shell | Resolution: 3.5→3.63 Å / Rmerge(I) obs: 0.399 / Num. unique all: 3956 / % possible all: 78.5 |
Reflection shell | *PLUS % possible obs: 78.5 % / Num. unique obs: 3956 / Mean I/σ(I) obs: 1.47 |
-Processing
Software |
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Refinement | Resolution: 3.5→40 Å / Details: This is a non-refined structure. | ||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.5→40 Å
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Refinement | *PLUS Highest resolution: 3.5 Å / Lowest resolution: 40 Å / Rfactor obs: 0.446 | ||||||||||||
Solvent computation | *PLUS | ||||||||||||
Displacement parameters | *PLUS | ||||||||||||
LS refinement shell | *PLUS Rfactor obs: 0.482 |