+Open data
-Basic information
Entry | Database: PDB / ID: 1qcq | |||||||||
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Title | UBIQUITIN CONJUGATING ENZYME | |||||||||
Components | PROTEIN (UBIQUITIN CONJUGATING ENZYME) | |||||||||
Keywords | LIGASE / UBIQUITIN / UBIQUITIN-CONJUGATING ENZYME / YEAST | |||||||||
Function / homology | Function and homology information Peroxisomal protein import / cytoplasm protein quality control by the ubiquitin-proteasome system / mitochondria-associated ubiquitin-dependent protein catabolic process / ubiquitin-dependent protein catabolic process via the multivesicular body sorting pathway / ribosome-associated ubiquitin-dependent protein catabolic process / E2 ubiquitin-conjugating enzyme / protein monoubiquitination / proteasome binding / ubiquitin conjugating enzyme activity / ubiquitin ligase complex ...Peroxisomal protein import / cytoplasm protein quality control by the ubiquitin-proteasome system / mitochondria-associated ubiquitin-dependent protein catabolic process / ubiquitin-dependent protein catabolic process via the multivesicular body sorting pathway / ribosome-associated ubiquitin-dependent protein catabolic process / E2 ubiquitin-conjugating enzyme / protein monoubiquitination / proteasome binding / ubiquitin conjugating enzyme activity / ubiquitin ligase complex / rescue of stalled ribosome / ubiquitin binding / protein polyubiquitination / ubiquitin-protein transferase activity / protein-macromolecule adaptor activity / ubiquitin-dependent protein catabolic process / protein ubiquitination / ubiquitin protein ligase binding / ATP binding / nucleus / cytoplasm Similarity search - Function | |||||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) | |||||||||
Method | X-RAY DIFFRACTION / Resolution: 2.7 Å | |||||||||
Authors | Cook, W.J. / Jeffrey, L.C. / Xu, Y. / Chau, V. | |||||||||
Citation | Journal: Biochemistry / Year: 1993 Title: Tertiary structures of class I ubiquitin-conjugating enzymes are highly conserved: crystal structure of yeast Ubc4. Authors: Cook, W.J. / Jeffrey, L.C. / Xu, Y. / Chau, V. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1qcq.cif.gz | 39.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1qcq.ent.gz | 27.7 KB | Display | PDB format |
PDBx/mmJSON format | 1qcq.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qc/1qcq ftp://data.pdbj.org/pub/pdb/validation_reports/qc/1qcq | HTTPS FTP |
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-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: 16474.715 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P15731, ubiquitin-protein ligase |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 4 |
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-Sample preparation
Crystal | Density Matthews: 3.11 Å3/Da / Density % sol: 60.51 % | |||||||||||||||||||||||||
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Crystal grow | Method: vapor diffusion, hanging drop / pH: 5.8 Details: PEG 8000, MAGNESIUM ACETATE, CACODYLATE, pH 5.8, VAPOR DIFFUSION, HANGING DROP | |||||||||||||||||||||||||
Crystal grow | *PLUS Method: vapor diffusion | |||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.5418 | ||||||||||||||||||||
Detector |
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Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 | ||||||||||||||||||||
Reflection | Resolution: 2.7→100 Å / Num. obs: 5940 / % possible obs: 97 % / Observed criterion σ(I): 0 / Redundancy: 3.8 % / Biso Wilson estimate: 37.5 Å2 / Rmerge(I) obs: 0.134 / Net I/σ(I): 10.2 | ||||||||||||||||||||
Reflection shell | Resolution: 2.7→2.87 Å / Redundancy: 2.2 % / Rmerge(I) obs: 0.368 / % possible all: 87 | ||||||||||||||||||||
Reflection | *PLUS Num. measured all: 22434 | ||||||||||||||||||||
Reflection shell | *PLUS % possible obs: 87 % |
-Processing
Software |
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Refinement | Resolution: 2.7→100 Å / Rfactor Rfree error: 0.016 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: ENGH & HUBER
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 25.84 Å2 / ksol: 0.31 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 24 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.7→100 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.7→2.87 Å / Rfactor Rfree error: 0.049 / Total num. of bins used: 6
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Xplor file | Serial no: 1 / Param file: PROTEIN_REP.PA / Topol file: PROTEIN.TOP | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Software | *PLUS Name: CNS / Version: 0.4 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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