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Yorodumi- PDB-5zdq: Crystal structure of cyanide-insensitive alternative oxidase from... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5zdq | ||||||
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Title | Crystal structure of cyanide-insensitive alternative oxidase from Trypanosoma brucei with COLLETOCHLORIN B | ||||||
Components | Alternative oxidase, mitochondrial | ||||||
Keywords | MEMBRANE PROTEIN / MEMBRANE BOUND DIIRON PROTEIN | ||||||
Function / homology | Function and homology information alternative oxidase activity / alternative respiration / Oxidoreductases / respirasome / ferric iron binding / mitochondrial inner membrane / oxidoreductase activity / mitochondrion Similarity search - Function | ||||||
Biological species | Trypanosoma brucei brucei (eukaryote) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å | ||||||
Authors | Shiba, T. / Inaoka, D.K. / Takahashi, G. / Tsuge, C. / Kido, Y. / Young, L. / Ueda, S. / Balogun, E.O. / Nara, T. / Honma, T. ...Shiba, T. / Inaoka, D.K. / Takahashi, G. / Tsuge, C. / Kido, Y. / Young, L. / Ueda, S. / Balogun, E.O. / Nara, T. / Honma, T. / Tanaka, A. / Inoue, M. / Saimoto, H. / Harada, S. / Moore, A.L. / Kita, K. | ||||||
Citation | Journal: Biochim Biophys Acta Bioenerg / Year: 2019 Title: Insights into the ubiquinol/dioxygen binding and proton relay pathways of the alternative oxidase. Authors: Shiba, T. / Inaoka, D.K. / Takahashi, G. / Tsuge, C. / Kido, Y. / Young, L. / Ueda, S. / Balogun, E.O. / Nara, T. / Honma, T. / Tanaka, A. / Inoue, M. / Saimoto, H. / Harada, S. / Moore, A.L. / Kita, K. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5zdq.cif.gz | 234.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5zdq.ent.gz | 186.6 KB | Display | PDB format |
PDBx/mmJSON format | 5zdq.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5zdq_validation.pdf.gz | 1.6 MB | Display | wwPDB validaton report |
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Full document | 5zdq_full_validation.pdf.gz | 1.6 MB | Display | |
Data in XML | 5zdq_validation.xml.gz | 43.2 KB | Display | |
Data in CIF | 5zdq_validation.cif.gz | 59.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zd/5zdq ftp://data.pdbj.org/pub/pdb/validation_reports/zd/5zdq | HTTPS FTP |
-Related structure data
Related structure data | 5zdpC 5zdrC 3vv9S S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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3 |
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Unit cell |
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Components on special symmetry positions |
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-Components
-Protein , 1 types, 4 molecules ABCD
#1: Protein | Mass: 37643.289 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Trypanosoma brucei brucei (eukaryote) / Gene: AOX / Plasmid: PET15B / Production host: Escherichia coli (E. coli) / Strain (production host): FN102 / References: UniProt: Q26710 |
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-Non-polymers , 6 types, 312 molecules
#2: Chemical | ChemComp-FE / #3: Chemical | ChemComp-OH / #4: Chemical | ChemComp-RNB / #5: Chemical | #6: Chemical | ChemComp-GOL / | #7: 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: 3.16 Å3/Da / Density % sol: 61.12 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.4 / Details: 30% PEG400, 0.1M IMIDAZOLE, 0.5M POTASSIUM FORMATE |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 0.9 Å | |||||||||||||||
Detector | Type: RAYONIX MX225HE / Detector: CCD / Date: Dec 4, 2012 | |||||||||||||||
Radiation | Monochromator: Si (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||
Radiation wavelength | Wavelength: 0.9 Å / Relative weight: 1 | |||||||||||||||
Reflection twin |
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Reflection | Resolution: 2.3→50 Å / Num. obs: 82140 / % possible obs: 99 % / Redundancy: 3.3 % / Rmerge(I) obs: 0.095 / Net I/σ(I): 7.7 | |||||||||||||||
Reflection shell | Resolution: 2.3→2.34 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.506 / Mean I/σ(I) obs: 2.6 / Num. unique obs: 4112 / % possible all: 99.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3VV9 Resolution: 2.3→42.89 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.936 / SU B: 3.676 / SU ML: 0.094 / Cross valid method: THROUGHOUT / ESU R: 0.043 / ESU R Free: 0.037 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 42.591 Å2
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Refinement step | Cycle: 1 / Resolution: 2.3→42.89 Å
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Refine LS restraints |
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