+Open data
-Basic information
Entry | Database: PDB / ID: 3w4y | ||||||
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Title | Crystal structure of yeast Erv1 core | ||||||
Components | Mitochondrial FAD-linked sulfhydryl oxidase ERV1 | ||||||
Keywords | OXIDOREDUCTASE / alpha helix / disulfide bond / redox / Tim40/Mia40 / mitochondria | ||||||
Function / homology | Function and homology information flavin-dependent sulfhydryl oxidase activity / thiol oxidase / thiol oxidase activity / protein import into mitochondrial intermembrane space / mitochondrial intermembrane space / flavin adenine dinucleotide binding / cellular response to oxidative stress / intracellular iron ion homeostasis / mitochondrion Similarity search - Function | ||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å | ||||||
Authors | Kawano, S. / Terao, K. / Watanabe, N. / Endo, T. | ||||||
Citation | Journal: To be published Title: Crystal structure of yeast Erv1 core Authors: Kawano, S. / Terao, K. / Watanabe, N. / Endo, T. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3w4y.cif.gz | 93.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3w4y.ent.gz | 71.8 KB | Display | PDB format |
PDBx/mmJSON format | 3w4y.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3w4y_validation.pdf.gz | 1.5 MB | Display | wwPDB validaton report |
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Full document | 3w4y_full_validation.pdf.gz | 1.5 MB | Display | |
Data in XML | 3w4y_validation.xml.gz | 18.6 KB | Display | |
Data in CIF | 3w4y_validation.cif.gz | 25.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/w4/3w4y ftp://data.pdbj.org/pub/pdb/validation_reports/w4/3w4y | HTTPS FTP |
-Related structure data
Related structure data | 2hj3S S: Starting model for refinement |
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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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Unit cell |
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-Components
#1: Protein | Mass: 14300.139 Da / Num. of mol.: 3 / Fragment: UNP RESIDUES 73-189 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Strain: ATCC 204508, S288c, W303-1A, / Gene: ERV1, ERV1/YGR029W, YGR029W / Plasmid: pET-15b / Production host: Escherichia coli (E. coli) / Strain (production host): SHUffle T7 / References: UniProt: P27882, thiol oxidase #2: Chemical | #3: 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: 61.56 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.4 Details: 10-20 % Polyethyleneglycole, 0.2-0.4 M citrate-Na, 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: BL38B1 / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: May 26, 2009 |
Radiation | Monochromator: Fixed exit Si (111) double crystal monochromator Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2→25.87 Å / Num. all: 37585 / Num. obs: 37584 / % possible obs: 99.9 % |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2HJ3 Resolution: 2→25.87 Å / Cor.coef. Fo:Fc: 0.93 / Cor.coef. Fo:Fc free: 0.912 / SU B: 3.442 / SU ML: 0.098 / Cross valid method: THROUGHOUT / ESU R: 0.162 / ESU R Free: 0.144 / Stereochemistry target values: MAXIMUM LIKELIHOOD / 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 / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 16.934 Å2
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Refinement step | Cycle: LAST / Resolution: 2→25.87 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2→2.052 Å / Total num. of bins used: 20
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