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- PDB-5bpz: Atomic-resolution structures of the APC/C subunits Apc4 and the A... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5bpz | ||||||
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Title | Atomic-resolution structures of the APC/C subunits Apc4 and the Apc5 N-terminal domain | ||||||
![]() | Anapc5 protein | ||||||
![]() | CELL CYCLE / Apc5 / APC/C / anaphase promoting complex | ||||||
Function / homology | Anaphase-promoting complex subunit 5 domain / Anaphase-promoting complex subunit 5 / Anaphase-promoting complex subunit 5 / anaphase-promoting complex / Armadillo-type fold / cell cycle / cell division / Anaphase-promoting complex subunit 5![]() | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Cronin, N. / Yang, J. / Zhang, Z. / Barford, D. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Atomic-Resolution Structures of the APC/C Subunits Apc4 and the Apc5 N-Terminal Domain. Authors: Cronin, N.B. / Yang, J. / Zhang, Z. / Kulkarni, K. / Chang, L. / Yamano, H. / Barford, D. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 73.5 KB | Display | ![]() |
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PDB format | ![]() | 54.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 438 KB | Display | ![]() |
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Full document | ![]() | 437.8 KB | Display | |
Data in XML | ![]() | 7.8 KB | Display | |
Data in CIF | ![]() | 9.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 19453.600 Da / Num. of mol.: 1 / Fragment: N-terminus, UNP residues 1-162 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() | ||
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#2: Chemical | #3: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.3 Å3/Da / Density % sol: 46.53 % / Description: Blocks |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7 Details: The protein was concentrated to 3.4 mg/mL. Plate-like crystals were grown in a buffer containing 40 mM sodium propionate, 20 mM sodium cacodylate, 40 mM Bis-Tris propane (pH 7.0) and 25% ...Details: The protein was concentrated to 3.4 mg/mL. Plate-like crystals were grown in a buffer containing 40 mM sodium propionate, 20 mM sodium cacodylate, 40 mM Bis-Tris propane (pH 7.0) and 25% PEG1500. Larger crystals were obtained by seeding. |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: May 1, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.0081 Å / Relative weight: 1 |
Reflection | Resolution: 2.18→63.63 Å / Num. all: 8213 / Num. obs: 8213 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 12.8 % / Rmerge(I) obs: 0.055 / Net I/σ(I): 28.5 |
Reflection shell | Resolution: 2.18→2.24 Å / Redundancy: 12.8 % / Rmerge(I) obs: 0.663 / Mean I/σ(I) obs: 4.5 / Num. unique all: 590 / % possible all: 99.1 |
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Processing
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Refinement | Resolution: 2.18→63 Å / Cor.coef. Fo:Fc: 0.9353 / Cor.coef. Fo:Fc free: 0.9208 / SU R Cruickshank DPI: 0.283 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.303 / SU Rfree Blow DPI: 0.195 / SU Rfree Cruickshank DPI: 0.192
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Displacement parameters | Biso max: 145.33 Å2 / Biso mean: 59.49 Å2 / Biso min: 27.89 Å2
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Refine analyze | Luzzati coordinate error obs: 0.372 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.18→63 Å
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LS refinement shell | Resolution: 2.2→2.46 Å / Total num. of bins used: 5
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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