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Yorodumi- PDB-1ej8: CRYSTAL STRUCTURE OF DOMAIN 2 OF THE YEAST COPPER CHAPERONE FOR S... -
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-Basic information
Entry | Database: PDB / ID: 1ej8 | ||||||
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Title | CRYSTAL STRUCTURE OF DOMAIN 2 OF THE YEAST COPPER CHAPERONE FOR SUPEROXIDE DISMUTASE (LYS7) AT 1.55 A RESOLUTION | ||||||
Components | LYS7 | ||||||
Keywords | CHAPERONE / beta barrel / copper chaperone for SOD / domain 2 | ||||||
Function / homology | Function and homology information superoxide dismutase complex / protein maturation by copper ion transfer / superoxide dismutase copper chaperone activity / Detoxification of Reactive Oxygen Species / copper ion transport / protein folding chaperone complex / removal of superoxide radicals / mitochondrial intermembrane space / mitochondrial inner membrane / copper ion binding ...superoxide dismutase complex / protein maturation by copper ion transfer / superoxide dismutase copper chaperone activity / Detoxification of Reactive Oxygen Species / copper ion transport / protein folding chaperone complex / removal of superoxide radicals / mitochondrial intermembrane space / mitochondrial inner membrane / copper ion binding / mitochondrion / nucleus / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) | ||||||
Method | X-RAY DIFFRACTION / Resolution: 1.55 Å | ||||||
Authors | Hall, L.T. / Sanchez, R.J. / Holloway, S.P. / Zhu, H. / Stine, J.E. / Lyons, T.J. / Demeler, B. / Schirf, V. / Hansen, J.C. / Nersissian, A.M. ...Hall, L.T. / Sanchez, R.J. / Holloway, S.P. / Zhu, H. / Stine, J.E. / Lyons, T.J. / Demeler, B. / Schirf, V. / Hansen, J.C. / Nersissian, A.M. / Valentine, J.S. / Hart, P.J. | ||||||
Citation | Journal: Biochemistry / Year: 2000 Title: X-ray crystallographic and analytical ultracentrifugation analyses of truncated and full-length yeast copper chaperones for SOD (LYS7): a dimer-dimer model of LYS7-SOD association and copper delivery. Authors: Hall, L.T. / Sanchez, R.J. / Holloway, S.P. / Zhu, H. / Stine, J.E. / Lyons, T.J. / Demeler, B. / Schirf, V. / Hansen, J.C. / Nersissian, A.M. / Valentine, J.S. / Hart, P.J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1ej8.cif.gz | 42.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1ej8.ent.gz | 28.7 KB | Display | PDB format |
PDBx/mmJSON format | 1ej8.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1ej8_validation.pdf.gz | 412.6 KB | Display | wwPDB validaton report |
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Full document | 1ej8_full_validation.pdf.gz | 414.4 KB | Display | |
Data in XML | 1ej8_validation.xml.gz | 9 KB | Display | |
Data in CIF | 1ej8_validation.cif.gz | 11.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ej/1ej8 ftp://data.pdbj.org/pub/pdb/validation_reports/ej/1ej8 | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 15462.370 Da / Num. of mol.: 1 / Fragment: DOMAIN 2 Source method: isolated from a genetically manipulated source Details: COPPER CHAPERONE FOR YEAST SOD Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Plasmid: PET3D / Production host: Escherichia coli (E. coli) / References: UniProt: P40202 |
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#2: Chemical | ChemComp-CA / |
#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: 1.89 Å3/Da / Density % sol: 34.92 % | ||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: PEG 400, CaCl2, Hepes, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K | ||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 4 ℃ / pH: 8 | ||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 298 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.5418 |
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Nov 15, 1998 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.55→90 Å / Num. all: 17662 / Num. obs: 17203 / % possible obs: 97.4 % / Observed criterion σ(I): -3 / Redundancy: 4.5 % / Biso Wilson estimate: 21.4 Å2 / Rmerge(I) obs: 0.054 / Net I/σ(I): 19.6 |
Reflection shell | Resolution: 1.55→1.61 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.346 / Num. unique all: 1530 / % possible all: 88.7 |
Reflection | *PLUS Num. measured all: 78174 |
Reflection shell | *PLUS % possible obs: 88.7 % |
-Processing
Software |
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Refinement | Resolution: 1.55→10 Å / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
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Refinement step | Cycle: LAST / Resolution: 1.55→10 Å
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Refine LS restraints |
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Software | *PLUS Name: SHELXL-97 / Classification: refinement | ||||||||||||||||||||
Refinement | *PLUS σ(F): 0 | ||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||
Refine LS restraints | *PLUS Type: s_angle_d / Dev ideal: 2.2 |