+Open data
-Basic information
Entry | Database: PDB / ID: 1gqp | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | APC10/DOC1 SUBUNIT OF S. cerevisiae | |||||||||
Components | DOC1/APC10 | |||||||||
Keywords | CELL CYCLE / APC10/DOC1 / APC/CYCLOSOME / UBIQUITINATION / E3 UBIQUITIN LIGASE / BETA SANDWICH / JELLY ROLL | |||||||||
Function / homology | Function and homology information anaphase-promoting complex / regulation of meiotic cell cycle / anaphase-promoting complex-dependent catabolic process / protein K11-linked ubiquitination / Antigen processing: Ubiquitination & Proteasome degradation / enzyme regulator activity / regulation of mitotic cell cycle / chromatin organization / protein ubiquitination / cell division / mitochondrion Similarity search - Function | |||||||||
Biological species | SACCHAROMYCES CEREVISIAE (brewer's yeast) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MIRAS / Resolution: 2.2 Å | |||||||||
Authors | Au, S.W.N. / Leng, X. / Harper, J.W.A.D.E. / Barford, D. | |||||||||
Citation | Journal: J.Mol.Biol. / Year: 2002 Title: Implications for the Ubiquitination Reaction of the Anaphase-Promoting Complex from the Crystal Structure of the Doc1/Apc10 Subunit. Authors: Au, S.W.N. / Leng, X. / Harper, J.W.A.D.E. / Barford, D. | |||||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 1gqp.cif.gz | 90.3 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb1gqp.ent.gz | 68.4 KB | Display | PDB format |
PDBx/mmJSON format | 1gqp.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gq/1gqp ftp://data.pdbj.org/pub/pdb/validation_reports/gq/1gqp | HTTPS FTP |
---|
-Related structure data
Similar structure data |
---|
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
| ||||||||
Noncrystallographic symmetry (NCS) | NCS oper: (Code: given Matrix: (0.62659, -0.77929, 0.009866), Vector: |
-Components
#1: Protein | Mass: 25627.854 Da / Num. of mol.: 2 / Fragment: RESIDUE 63-283 Source method: isolated from a genetically manipulated source Source: (gene. exp.) SACCHAROMYCES CEREVISIAE (brewer's yeast) Plasmid: PET28M / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): B834 / References: UniProt: P53068 #2: Chemical | ChemComp-BR / #3: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 2 |
---|
-Sample preparation
Crystal | Density Matthews: 2.67 Å3/Da / Density % sol: 53.87 % | |||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Crystal grow | pH: 4.6 Details: 0.1M SODIUM ACETATE, 0.3M LITHIUM BROMIDE AND 2M SODIUM FORMATE, PH 4.6 | |||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 20 ℃ / Method: vapor diffusion, hanging drop / pH: 4.6 | |||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
|
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: ELETTRA / Beamline: 5.2R / Wavelength: 0.92 |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Jun 10, 2001 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.92 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→50 Å / Num. obs: 27256 / % possible obs: 99.9 % / Observed criterion σ(I): 2 / Biso Wilson estimate: 18.2 Å2 / Rmerge(I) obs: 0.058 / Net I/σ(I): 22.9 |
Reflection shell | Resolution: 2.2→2.28 Å / Rmerge(I) obs: 0.28 / % possible all: 99 |
Reflection | *PLUS Lowest resolution: 50 Å / Num. measured all: 310219 |
Reflection shell | *PLUS Highest resolution: 2.2 Å / % possible obs: 99 % / Rmerge(I) obs: 0.278 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MIRAS / Resolution: 2.2→46.24 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 1821783.21 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 Details: RESIDUES C-TERMINAL OF 256 IN CHAINS A AND B ARE DISORDERED.
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Solvent model: FLAT MODEL / Bsol: 53.9592 Å2 / ksol: 0.376842 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 34 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.2→46.24 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2→2.13 Å / Total num. of bins used: 6 /
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Xplor file |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Lowest resolution: 50 Å / % reflection Rfree: 5 % / Rfactor obs: 0.2109 / Rfactor Rfree: 0.245 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | *PLUS Highest resolution: 2.2 Å / Lowest resolution: 2.28 Å |