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Yorodumi- PDB-3vva: Crystal structure of cyanide-insensitive alternative oxidase from... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3vva | ||||||
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Title | Crystal structure of cyanide-insensitive alternative oxidase from Trypanosoma brucei with ascofuranone derivative | ||||||
Components | Alternative oxidase, mitochondrial | ||||||
Keywords | OXIDOREDUCTASE/OXIDOREDUCTASE INHIBITOR / HELIX DOUBLE / MEMBRANE BOUND DIIRON PROTEIN / OXIDASE / MEMBRANE / OXIDOREDUCTASE / OXIDOREDUCTASE-OXIDOREDUCTASE INHIBITOR COMPLEX / ALTERNATIVE OXIDASE | ||||||
Function / homology | Function and homology information alternative oxidase activity / 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: 2.59 Å | ||||||
Authors | Shiba, T. / Kido, Y. / Sakamoto, K. / Inaoka, D.K. / Tsuge, C. / Tatsumi, R. / Balogun, E.O. / Nara, T. / Aoki, T. / Honma, T. ...Shiba, T. / Kido, Y. / Sakamoto, K. / Inaoka, D.K. / Tsuge, C. / Tatsumi, R. / Balogun, E.O. / Nara, T. / Aoki, T. / Honma, T. / Tanaka, A. / Inoue, M. / Matsuoka, S. / Saimoto, H. / Moore, A.L. / Harada, S. / Kita, K. | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2013 Title: Structure of the trypanosome cyanide-insensitive alternative oxidase Authors: Shiba, T. / Kido, Y. / Sakamoto, K. / Inaoka, D.K. / Tsuge, C. / Tatsumi, R. / Takahashi, G. / Balogun, E.O. / Nara, T. / Aoki, T. / Honma, T. / Tanaka, A. / Inoue, M. / Matsuoka, S. / ...Authors: Shiba, T. / Kido, Y. / Sakamoto, K. / Inaoka, D.K. / Tsuge, C. / Tatsumi, R. / Takahashi, G. / Balogun, E.O. / Nara, T. / Aoki, T. / Honma, T. / Tanaka, A. / Inoue, M. / Matsuoka, S. / Saimoto, H. / Moore, A.L. / Harada, S. / Kita, K. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3vva.cif.gz | 230.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3vva.ent.gz | 184.4 KB | Display | PDB format |
PDBx/mmJSON format | 3vva.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vv/3vva ftp://data.pdbj.org/pub/pdb/validation_reports/vv/3vva | HTTPS FTP |
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-Related structure data
Related structure data | 3vv9SC 3w54C 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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2 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#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 #2: Chemical | ChemComp-FE / #3: Chemical | ChemComp-OH / #4: Chemical | ChemComp-CHW / #5: 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: 3.2 Å3/Da / Density % sol: 61.55 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.4 Details: 30% PEG 400, 0.1M IMIDAZOLE, 0.5M POTASSIUM FORMATE, pH 7.4, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-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: Jul 16, 2010 | |||||||||||||||
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: 2.59→50 Å / Num. all: 57960 / Num. obs: 54110 / % possible obs: 93.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 2.5 % / Rmerge(I) obs: 0.124 / Net I/σ(I): 8.6 | |||||||||||||||
Reflection shell | Resolution: 2.59→2.64 Å / Rmerge(I) obs: 0.614 / Mean I/σ(I) obs: 1.3 / % possible all: 85.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3VV9 Resolution: 2.59→39.81 Å / Cor.coef. Fo:Fc: 0.925 / Cor.coef. Fo:Fc free: 0.902 / SU B: 5.377 / SU ML: 0.129 / Cross valid method: THROUGHOUT / ESU R: 0.092 / ESU R Free: 0.061 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 42.779 Å2
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Refinement step | Cycle: LAST / Resolution: 2.59→39.81 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.59→2.657 Å / Total num. of bins used: 20
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