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Yorodumi- PDB-1q34: Crystal structures of two UBC (E2) enzymes of the ubiquitin-conju... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1q34 | ||||||
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Title | Crystal structures of two UBC (E2) enzymes of the ubiquitin-conjugating system in Caenorhabditis elegans | ||||||
Components | Ubiquitin-conjugating enzyme E2-21.5 kDa | ||||||
Keywords | LIGASE / alpha-beta(4)-alpha(3) / core: meander beta-sheet plus one helix 2 / Structural Genomics / PSI / Protein Structure Initiative / Southeast Collaboratory for Structural Genomics / SECSG | ||||||
Function / homology | Function and homology information Synthesis of active ubiquitin: roles of E1 and E2 enzymes / Antigen processing: Ubiquitination & Proteasome degradation / HULC complex / ubiquitin conjugating enzyme complex / E2 ubiquitin-conjugating enzyme / ubiquitin conjugating enzyme activity / protein polyubiquitination / proteasome-mediated ubiquitin-dependent protein catabolic process / protein ubiquitination / DNA repair ...Synthesis of active ubiquitin: roles of E1 and E2 enzymes / Antigen processing: Ubiquitination & Proteasome degradation / HULC complex / ubiquitin conjugating enzyme complex / E2 ubiquitin-conjugating enzyme / ubiquitin conjugating enzyme activity / protein polyubiquitination / proteasome-mediated ubiquitin-dependent protein catabolic process / protein ubiquitination / DNA repair / ubiquitin protein ligase binding / ATP binding Similarity search - Function | ||||||
Biological species | Caenorhabditis elegans (invertebrata) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å | ||||||
Authors | Schormann, N. / Lin, G. / Li, S. / Symersky, J. / Qiu, S. / Finley, J. / Luo, D. / Stanton, A. / Carson, M. / Luo, M. / Southeast Collaboratory for Structural Genomics (SECSG) | ||||||
Citation | Journal: To be Published Title: Crystal structures of two UBC (E2) enzymes of the ubiquitin-conjugating system in Caenorhabditis elegans Authors: Schormann, N. / Lin, G. / Li, S. / Symersky, J. / Qiu, S. / Finley, J. / Luo, D. / Stanton, A. / Carson, M. / Luo, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1q34.cif.gz | 99 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1q34.ent.gz | 76.6 KB | Display | PDB format |
PDBx/mmJSON format | 1q34.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/q3/1q34 ftp://data.pdbj.org/pub/pdb/validation_reports/q3/1q34 | HTTPS FTP |
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-Related structure data
Related structure data | 1pzvC 2aakS C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data | |
Other databases |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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3 |
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Unit cell |
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-Components
#1: Protein | Mass: 18612.732 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Caenorhabditis elegans (invertebrata) / Gene: UBC-1 OR C35B1.1 / Plasmid: pET28b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P52478, ubiquitin-protein ligase #2: 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: 3.12 Å3/Da / Density % sol: 60.64 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 9.6 Details: PEG 8000, Calcium Acetate, Glycerol, Glycine, pH 9.6, VAPOR DIFFUSION, HANGING DROP, temperature 295K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1.072 Å |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Nov 10, 2002 / Details: Mirrors |
Radiation | Monochromator: Double Crystal Monochromator Si-220 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.072 Å / Relative weight: 1 |
Reflection | Resolution: 2.77→50 Å / Num. all: 17357 / Num. obs: 17357 / % possible obs: 95.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.9 % / Biso Wilson estimate: 70.6 Å2 / Rmerge(I) obs: 0.039 / Net I/σ(I): 16.2 |
Reflection shell | Resolution: 2.77→2.87 Å / % possible all: 83.1 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2AAK Resolution: 2.9→19.74 Å / Rfactor Rfree error: 0.01 / Data cutoff high absF: 323096.58 / Data cutoff high rms absF: 323096.58 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 1 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 34.7609 Å2 / ksol: 0.290883 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 68 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.9→19.74 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.9→3.08 Å / Rfactor Rfree error: 0.035 / Total num. of bins used: 6
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Xplor file |
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