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Open data
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Basic information
Entry | Database: PDB / ID: 2ggt | ||||||
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Title | Crystal structure of human SCO1 complexed with nickel. | ||||||
![]() | SCO1 protein homolog, mitochondrial![]() | ||||||
![]() | ![]() ![]() ![]() ![]() | ||||||
Function / homology | ![]() copper chaperone activity / mitochondrial cytochrome c oxidase assembly / Respiratory electron transport / ![]() ![]() ![]() Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Banci, L. / Bertini, I. / Calderone, V. / Ciofi-Baffoni, S. / Mangani, S. / Martinelli, M. / Palumaa, P. / Wang, S. | ||||||
![]() | ![]() Title: A hint for the function of human Sco1 from different structures. Authors: Banci, L. / Bertini, I. / Calderone, V. / Ciofi-Baffoni, S. / Mangani, S. / Martinelli, M. / Palumaa, P. / Wang, S. #1: ![]() Title: Crystal structure of human SCO1: implications for redox signaling by a mitochondrial cytochrome c oxidase 'assembly' protein. Authors: Williams, J.C. / Sue, C. / Banting, G.S. / Yang, H. / Glerum, D.M. / Hendrickson, W.A. / Schon, E.A. #2: ![]() Title: Solution structure of Sco1: a thioredoxin-like protein Involved in cytochrome c oxidase assembly. Authors: Balatri, E. / Banci, L. / Bertini, I. / Cantini, F. / Ciofi-Baffoni, S. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 81.3 KB | Display | ![]() |
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PDB format | ![]() | 60.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 2gqkC ![]() 2gqlC ![]() 2gqmC ![]() 2gt5C ![]() 2gt6C ![]() 2gvpC ![]() 1wp0S S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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2 | ![]()
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Unit cell |
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Details | The protein is monomeric in vivo but there are two molecules in the asymmetric unit. |
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Components
#1: Protein | ![]() Mass: 18748.135 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() #2: Chemical | ![]() #3: Chemical | ![]() #4: Water | ChemComp-HOH / | ![]() |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.45 Å3/Da / Density % sol: 49.86 % |
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Crystal grow![]() | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: 0.1 Tris-HCl, 25% PEG6000, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Nov 30, 2005 Details: Channel-cut silicon monochromator and cylindrical grazing incidence mirror |
Radiation | Monochromator: Channel-cut silicon monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 2.4→78.2 Å / Num. all: 14686 / Num. obs: 14686 / % possible obs: 97.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.2 % / Biso Wilson estimate: 46.78 Å2 / Rmerge(I) obs: 0.092 / Rsym value: 0.092 / Net I/σ(I): 6.8 |
Reflection shell | Resolution: 2.4→2.53 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.455 / Mean I/σ(I) obs: 1.6 / Num. unique all: 5541 / Rsym value: 0.455 / % possible all: 81.5 |
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Processing
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Refinement | Method to determine structure![]() ![]() Starting model: 1wp0 Resolution: 2.4→36.74 Å / Cor.coef. Fo:Fc: 0.929 / Cor.coef. Fo:Fc free: 0.869 / SU B: 10.831 / SU ML: 0.257 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.548 / ESU R Free: 0.353 / 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: 36.655 Å2
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Refine analyze | Luzzati sigma a obs: 0.257 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.4→36.74 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.397→2.459 Å / Total num. of bins used: 20
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