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Open data
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Basic information
Entry | Database: PDB / ID: 1x23 | ||||||
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Title | Crystal structure of ubch5c | ||||||
![]() | Ubiquitin-conjugating enzyme E2 D3 | ||||||
![]() | LIGASE / Ubiquitin conjugating enzyme / Ubiquitin / E2 | ||||||
Function / homology | ![]() (E3-independent) E2 ubiquitin-conjugating enzyme / Signaling by BMP / protein K6-linked ubiquitination / protein K11-linked ubiquitination / positive regulation of protein targeting to mitochondrion / E2 ubiquitin-conjugating enzyme / protein monoubiquitination / ubiquitin conjugating enzyme activity / negative regulation of BMP signaling pathway / protein autoubiquitination ...(E3-independent) E2 ubiquitin-conjugating enzyme / Signaling by BMP / protein K6-linked ubiquitination / protein K11-linked ubiquitination / positive regulation of protein targeting to mitochondrion / E2 ubiquitin-conjugating enzyme / protein monoubiquitination / ubiquitin conjugating enzyme activity / negative regulation of BMP signaling pathway / protein autoubiquitination / protein K48-linked ubiquitination / ubiquitin ligase complex / TICAM1, RIP1-mediated IKK complex recruitment / IKK complex recruitment mediated by RIP1 / Negative regulators of DDX58/IFIH1 signaling / Peroxisomal protein import / Downregulation of SMAD2/3:SMAD4 transcriptional activity / Regulation of TNFR1 signaling / protein modification process / Oxygen-dependent proline hydroxylation of Hypoxia-inducible Factor Alpha / Inactivation of CSF3 (G-CSF) signaling / protein polyubiquitination / ubiquitin-protein transferase activity / ubiquitin protein ligase activity / Antigen processing: Ubiquitination & Proteasome degradation / E3 ubiquitin ligases ubiquitinate target proteins / Neddylation / ubiquitin-dependent protein catabolic process / proteasome-mediated ubiquitin-dependent protein catabolic process / endosome membrane / protein ubiquitination / DNA repair / apoptotic process / ubiquitin protein ligase binding / negative regulation of transcription by RNA polymerase II / extracellular exosome / nucleoplasm / ATP binding / nucleus / plasma membrane / cytosol Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Nakanishi, M. / Teshima, N. / Mizushima, T. / Murata, S. / Tanaka, K. / Yamane, T. | ||||||
![]() | ![]() Title: Crystal structure of ubch5c Authors: Nakanishi, M. / Teshima, N. / Mizushima, T. / Murata, S. / Tanaka, K. / Yamane, T. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 145.4 KB | Display | ![]() |
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PDB format | ![]() | 114.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 457.1 KB | Display | ![]() |
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Full document | ![]() | 470.8 KB | Display | |
Data in XML | ![]() | 33.9 KB | Display | |
Data in CIF | ![]() | 49 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1qcqS S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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2 | ![]()
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3 | ![]()
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4 | ![]()
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: MET / Beg label comp-ID: MET / End auth comp-ID: MET / End label comp-ID: MET / Refine code: 5 / Auth seq-ID: 1 - 147 / Label seq-ID: 9 - 155
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Components
#1: Protein | Mass: 17490.996 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2 Å3/Da / Density % sol: 38.1 % |
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Crystal grow | Temperature: 288 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 0.1M HEPES-Na, 10% iso-propanol, 20% PEG4000, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 288K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: Bruker DIP-6040 / Detector: CCD / Date: Nov 27, 2004 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→100 Å / Num. obs: 46077 / % possible obs: 93.9 % / Observed criterion σ(I): 0 / Redundancy: 2.8 % / Biso Wilson estimate: 21.7 Å2 / Rmerge(I) obs: 0.04 / Net I/σ(I): 20.9 |
Reflection shell | Resolution: 1.8→1.86 Å / Rmerge(I) obs: 0.249 / % possible all: 83.8 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1QCQ Resolution: 1.85→20 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.902 / SU B: 4.156 / SU ML: 0.132 / Cross valid method: THROUGHOUT / ESU R: 0.207 / ESU R Free: 0.199 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 28.5 Å2
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Refinement step | Cycle: LAST / Resolution: 1.85→20 Å
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Refine LS restraints |
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Refine LS restraints NCS | Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION
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LS refinement shell | Resolution: 1.85→1.898 Å / Total num. of bins used: 20
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