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Yorodumi- PDB-8ew8: Crystal structure of Saccharomyces cerevisiae Altered Inheritance... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8ew8 | ||||||||||||
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Title | Crystal structure of Saccharomyces cerevisiae Altered Inheritance rate of Mitochondria protein 18 (AIM18p) R123A mutant | ||||||||||||
Components | Altered inheritance of mitochondria protein 18, mitochondrial | ||||||||||||
Keywords | UNKNOWN FUNCTION / Altered inheritance of mitochondria protein 18 / mitochondrial protein / YHR198C / FMP22 | ||||||||||||
Function / homology | Chalcone isomerase like / intramolecular lyase activity / Chalcone isomerase, 3-layer sandwich / Chalcone isomerase / Chalcone isomerase superfamily / mitochondrion / Altered inheritance of mitochondria protein 18, mitochondrial Function and homology information | ||||||||||||
Biological species | Saccharomyces cerevisiae S288C (yeast) | ||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.15 Å | ||||||||||||
Authors | Bingman, C.A. / Schmitz, J.M. / Smith, R.W. / Pagliarini, D.J. | ||||||||||||
Funding support | United States, 3items
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Citation | Journal: J.Biol.Chem. / Year: 2023 Title: Aim18p and Aim46p are chalcone isomerase domain-containing mitochondrial hemoproteins in Saccharomyces cerevisiae. Authors: Schmitz, J.M. / Wolters, J.F. / Murray, N.H. / Guerra, R.M. / Bingman, C.A. / Hittinger, C.T. / Pagliarini, D.J. | ||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8ew8.cif.gz | 184 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8ew8.ent.gz | 126.8 KB | Display | PDB format |
PDBx/mmJSON format | 8ew8.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8ew8_validation.pdf.gz | 430 KB | Display | wwPDB validaton report |
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Full document | 8ew8_full_validation.pdf.gz | 429.9 KB | Display | |
Data in XML | 8ew8_validation.xml.gz | 11.7 KB | Display | |
Data in CIF | 8ew8_validation.cif.gz | 16 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ew/8ew8 ftp://data.pdbj.org/pub/pdb/validation_reports/ew/8ew8 | HTTPS FTP |
-Related structure data
Related structure data | 8ew9C C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 28208.270 Da / Num. of mol.: 1 / Mutation: R123A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae S288C (yeast) / Strain: ATCC 204508 / S288c / Gene: AIM18, FMP22, YHR198C / Production host: Escherichia coli (E. coli) / References: UniProt: P38884 | ||||
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#2: Chemical | ChemComp-SO4 / #3: Water | ChemComp-HOH / | Has ligand of interest | N | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 4.5 Å3/Da / Density % sol: 72.71 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: Crystals for data collection were obtained by mixing 200 nL of protein soiution (15.1 mg/mL Nd70 R123A Aim18p, 20 mM HEPES buffer, pH 7.5, 200 mM NaCl, 2 mM TCEP) with 150 nL of reservoir ...Details: Crystals for data collection were obtained by mixing 200 nL of protein soiution (15.1 mg/mL Nd70 R123A Aim18p, 20 mM HEPES buffer, pH 7.5, 200 mM NaCl, 2 mM TCEP) with 150 nL of reservoir solution (26% PEG 3350, 200 mM Li2SO4, 100 mM HEPES pH 7.5) in a SD2 crystallization tray with a TTP Labtech Mosquito crystallization robot. Crystals were cryoprotected with reservoir solution supplemented to 30% PEG 3350 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | ||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 0.964370, 0.979370, 0.979610 | ||||||||||||
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Feb 7, 2018 | ||||||||||||
Radiation | Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||
Radiation wavelength |
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Reflection | Resolution: 2.15→48.7 Å / Num. obs: 27153 / % possible obs: 97.59 % / Redundancy: 18.8 % / Biso Wilson estimate: 40.56 Å2 / CC1/2: 0.999 / CC star: 1 / Rmerge(I) obs: 0.09783 / Rpim(I) all: 0.02266 / Rrim(I) all: 0.1005 / Net I/σ(I): 21.8 | ||||||||||||
Reflection shell | Resolution: 2.15→2.227 Å / Redundancy: 12.3 % / Rmerge(I) obs: 0.9956 / Mean I/σ(I) obs: 2.38 / Num. unique obs: 2241 / CC1/2: 0.702 / CC star: 0.908 / Rpim(I) all: 0.2836 / Rrim(I) all: 1.039 / % possible all: 81.11 |
-Processing
Software |
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Refinement | Method to determine structure: MAD / Resolution: 2.15→48.7 Å / SU ML: 0.265 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.8387 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 51.38 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.15→48.7 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group | Refine-ID: X-RAY DIFFRACTION / Auth asym-ID: A / Label asym-ID: A
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