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Yorodumi- PDB-4x57: Structure of an Arabidopsis E2 / Membrane-anchored Ubiquitin-fold... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4x57 | ||||||
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Title | Structure of an Arabidopsis E2 / Membrane-anchored Ubiquitin-fold Protein Complex | ||||||
Components |
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Keywords | ligase/protein binding / Ubiquitin / Ubconjugating (E2) enzymes / Membrane anchored / Ubiquitin-fold protein 3 / MUB3 / E1:E2 Complex / ligase-protein binding complex | ||||||
Function / homology | Function and homology information endosperm development / E2 ubiquitin-conjugating enzyme / ubiquitin conjugating enzyme activity / protein polyubiquitination / ubiquitin-protein transferase activity / ubiquitin-dependent protein catabolic process / ATP binding / nucleus / plasma membrane / cytoplasm Similarity search - Function | ||||||
Biological species | Arabidopsis thaliana (thale cress) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å | ||||||
Authors | Korolev, S. / Koroleva, O. / Lu, X. / Downes, B. | ||||||
Funding support | United States, 1items
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Citation | Journal: To Be Published Title: Structure of an Arabidopsis E2 / Membrane-anchored Ubiquitin-fold ProteinComplex Authors: Korolev, S. / Koroleva, O. / Lu, X. / Downes, B. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4x57.cif.gz | 110.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4x57.ent.gz | 82.9 KB | Display | PDB format |
PDBx/mmJSON format | 4x57.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4x57_validation.pdf.gz | 480.6 KB | Display | wwPDB validaton report |
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Full document | 4x57_full_validation.pdf.gz | 490.5 KB | Display | |
Data in XML | 4x57_validation.xml.gz | 19.4 KB | Display | |
Data in CIF | 4x57_validation.cif.gz | 25.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/x5/4x57 ftp://data.pdbj.org/pub/pdb/validation_reports/x5/4x57 | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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2 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: 1 / Refine code: 2
NCS ensembles :
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-Components
#1: Protein | Mass: 19819.713 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: UBC8, UBC4A, At5g41700, MBK23.24 / Production host: Escherichia coli (E. coli) / References: UniProt: P35131, ubiquitin-protein ligase #2: Protein | Mass: 15026.398 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: MUB3, At4g24990, F13M23.130 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9SW27 #3: Chemical | ChemComp-SO4 / |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 3.86 Å3/Da / Density % sol: 68.1 % |
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Crystal grow | Temperature: 280 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 3.0 M (NH4)2SO4 / PH range: 7.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 0.97934 Å |
Detector | Type: RAYONIX MX-300 / Detector: CCD / Date: Apr 20, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97934 Å / Relative weight: 1 |
Reflection | Resolution: 2.8→50 Å / Num. obs: 27721 / % possible obs: 99.8 % / Observed criterion σ(I): -3 / Redundancy: 7.2 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 30 |
Reflection shell | Resolution: 2.8→2.85 Å / Redundancy: 7.3 % / Rmerge(I) obs: 1 / Mean I/σ(I) obs: 1.95 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY ID 3NOB, 1QCQ Resolution: 2.8→10 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.913 / SU B: 13.175 / SU ML: 0.248 / Cross valid method: THROUGHOUT / ESU R: 0.38 / ESU R Free: 0.283 / 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: 75.553 Å2
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Refinement step | Cycle: LAST / Resolution: 2.8→10 Å
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Refine LS restraints |
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