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Yorodumi- PDB-1z3d: Protein crystal growth improvement leading to the 2.5A crystallog... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1z3d | ||||||
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Title | Protein crystal growth improvement leading to the 2.5A crystallographic structure of ubiquitin-conjugating enzyme (ubc-1) from Caenorhabditis elegans | ||||||
Components | Ubiquitin-conjugating enzyme E2 1 | ||||||
Keywords | LIGASE / E2 / Ubiquitination / Ubiquitin-conjugating / crystal growth / 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 / molecular replacement / Resolution: 2.5 Å | ||||||
Authors | Gavira, J.A. / DiGiammarino, E. / Tempel, W. / Toh, D. / Liu, Z.J. / Wang, B.C. / Meehan, E. / Ng, J.D. / Southeast Collaboratory for Structural Genomics (SECSG) | ||||||
Citation | Journal: To be Published Title: Protein crystal growth improvement leading to the 2.5A crystallographic structure of ubiquitin-conjugating enzyme (ubc-1) from Caenorhabditis elegans Authors: Gavira, J.A. / DiGiammarino, E. / Tempel, W. / Toh, D. / Liu, Z.J. / Wang, B.C. / Meehan, E. / Ng, J.D. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1z3d.cif.gz | 43.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1z3d.ent.gz | 29.8 KB | Display | PDB format |
PDBx/mmJSON format | 1z3d.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/z3/1z3d ftp://data.pdbj.org/pub/pdb/validation_reports/z3/1z3d | HTTPS FTP |
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-Related structure data
Related structure data | 2aakS 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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Unit cell |
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-Components
#1: Protein | Mass: 17952.020 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Caenorhabditis elegans (invertebrata) / Gene: ubc-1 / Plasmid: pET26 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: P52478, ubiquitin-protein ligase |
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#2: 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: 3 Å3/Da / Density % sol: 59 % |
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Crystal grow | Temperature: 277.5 K / Method: counter-diffusion / pH: 8.5 Details: 0.1 M Tris, pH 8.5, 0.2 M MgCl2, 30% PEG 4K, counter-diffusion, temperature 277.5K |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 0.97 Å | |||||||||||||||||||||||||||||||||
Detector | Type: MAR CCD 165 mm / Detector: CCD | |||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.97 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.5→50 Å / Num. obs: 7370 / % possible obs: 97.1 % / Redundancy: 2.6 % / Biso Wilson estimate: 50.5 Å2 / Rmerge(I) obs: 0.058 | |||||||||||||||||||||||||||||||||
Reflection shell |
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-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2aak Resolution: 2.5→29.03 Å / Rfactor Rfree error: 0.01 / Data cutoff high absF: 1342948.77 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 17.8198 Å2 / ksol: 0.321999 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 41 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.5→29.03 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.5→2.66 Å / Rfactor Rfree error: 0.038 / Total num. of bins used: 6
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Xplor file |
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