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Yorodumi- PDB-6bxw: Crystal structure of Toxoplasma gondii Mitochondrial Association ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6bxw | ||||||
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Title | Crystal structure of Toxoplasma gondii Mitochondrial Association Factor 1 B (MAF1B) in complex with ADPribose | ||||||
Components | Mitochondrial association factor 1 | ||||||
Keywords | MEMBRANE PROTEIN / macro domain / ADPribose / neofuntionality | ||||||
Function / homology | symbiont-containing vacuole membrane / cytoplasmic vesicle membrane / ADENOSINE-5-DIPHOSPHORIBOSE / Mitochondrial association factor 1 form b1 Function and homology information | ||||||
Biological species | Toxoplasma gondii (eukaryote) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.65 Å | ||||||
Authors | Parker, M.L. / Ramaswamy, R. / Boulanger, M.J. | ||||||
Funding support | Canada, 1items
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Citation | Journal: Mol. Microbiol. / Year: 2018 Title: A Toxoplasma gondii locus required for the direct manipulation of host mitochondria has maintained multiple ancestral functions. Authors: Blank, M.L. / Parker, M.L. / Ramaswamy, R. / Powell, C.J. / English, E.D. / Adomako-Ankomah, Y. / Pernas, L.F. / Workman, S.D. / Boothroyd, J.C. / Boulanger, M.J. / Boyle, J.P. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6bxw.cif.gz | 69.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6bxw.ent.gz | 48 KB | Display | PDB format |
PDBx/mmJSON format | 6bxw.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bx/6bxw ftp://data.pdbj.org/pub/pdb/validation_reports/bx/6bxw | HTTPS FTP |
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-Related structure data
Related structure data | 6bxrSC 6bxsC 6bxtC 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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Unit cell |
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-Components
#1: Protein | Mass: 29487.172 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Toxoplasma gondii (eukaryote) / Gene: MAF1 / Plasmid: pET28A / Production host: Escherichia coli (E. coli) / References: UniProt: A0A140H546 |
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#2: Chemical | ChemComp-APR / |
#3: 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: 2.16 Å3/Da / Density % sol: 42.95 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 0.2 M ammonium sulfate, 20% PEG3350 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.9795 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 5, 2012 / Details: Flat Si Rh coated M0 |
Radiation | Monochromator: Liquid nitrogen-cooled double crystal Si(111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 1.65→40.556 Å / Num. obs: 29065 / % possible obs: 93.4 % / Redundancy: 3.9 % / CC1/2: 0.991 / Rmerge(I) obs: 0.094 / Net I/σ(I): 7.6 |
Reflection shell | Resolution: 1.65→1.68 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.553 / Mean I/σ(I) obs: 2.2 / % possible all: 97.4 |
-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6BXR Resolution: 1.65→40.556 Å / SU ML: 0.15 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 21.75
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 87.62 Å2 / Biso mean: 22.7313 Å2 / Biso min: 8.6 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.65→40.556 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 10
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