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Open data
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Basic information
Entry | Database: PDB / ID: 3ehv | ||||||
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Title | X-ray structure of human ubiquitin Zn(II) adduct | ||||||
![]() | Ubiquitin![]() | ||||||
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Function / homology | ![]() Peptide chain elongation / Selenocysteine synthesis / Formation of a pool of free 40S subunits / SRP-dependent cotranslational protein targeting to membrane / Eukaryotic Translation Termination / Response of EIF2AK4 (GCN2) to amino acid deficiency / Viral mRNA Translation / Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) / GTP hydrolysis and joining of the 60S ribosomal subunit / Major pathway of rRNA processing in the nucleolus and cytosol ...Peptide chain elongation / Selenocysteine synthesis / Formation of a pool of free 40S subunits / SRP-dependent cotranslational protein targeting to membrane / Eukaryotic Translation Termination / Response of EIF2AK4 (GCN2) to amino acid deficiency / Viral mRNA Translation / Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) / GTP hydrolysis and joining of the 60S ribosomal subunit / Major pathway of rRNA processing in the nucleolus and cytosol / L13a-mediated translational silencing of Ceruloplasmin expression / protein modification process => GO:0036211 / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / cytosolic ribosome / ![]() ![]() ![]() Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Falini, G. / Fermani, S. / Tosi, G. | ||||||
![]() | ![]() Title: Structural probing of Zn(II), Cd(II) and Hg(II) binding to human ubiquitin. Authors: Falini, G. / Fermani, S. / Tosi, G. / Arnesano, F. / Natile, G. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 52 KB | Display | ![]() |
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PDB format | ![]() | 41 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 299.7 KB | Display | ![]() |
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Full document | ![]() | 305.3 KB | Display | |
Data in XML | ![]() | 12.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3eecC ![]() 3efuC ![]() 1ubqS 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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2 | ![]()
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3 | ![]()
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Unit cell |
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Components
#1: Protein | ![]() Mass: 8576.831 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() References: UniProt: P62988, UniProt: P0CG48*PLUS, ![]() #2: Chemical | ChemComp-ZN / | #3: Water | ChemComp-HOH / | ![]() |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.05 Å3/Da / Density % sol: 39.97 % |
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Crystal grow![]() | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 25% (w/v) PEG 1450, 50mM HEPES pH 7.0, 25mM zinc acetate, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MAR CCD 165 mm / Detector: CCD / Date: May 26, 2007 |
Radiation | Monochromator: double-crystal Si(111) monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 1.8→32.5 Å / Num. all: 19140 / Num. obs: 19094 / % possible obs: 94.8 % / Observed criterion σ(I): 5 / Redundancy: 3.7 % / Biso Wilson estimate: 17.2 Å2 / Rmerge(I) obs: 0.0101 / Rsym value: 0.114 / Net I/σ(I): 11.7 |
Reflection shell | Resolution: 1.8→1.84 Å / Redundancy: 1.4 % / Rmerge(I) obs: 0.081 / Mean I/σ(I) obs: 1.3 / Num. unique all: 302 / Rsym value: 0.513 / % possible all: 30.9 |
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Processing
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Refinement | Method to determine structure![]() ![]() Starting model: 1UBQ Resolution: 1.81→32.15 Å / Rfactor Rfree error: 0.009 / Data cutoff high absF: 3191116.77 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(I): 5 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 66.0679 Å2 / ksol: 0.353035 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 25.8 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.81→32.15 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.8→1.91 Å / Rfactor Rfree error: 0.034 / Total num. of bins used: 6
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Xplor file |
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