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Yorodumi- PDB-5h7r: Structural basis of the flanking zinc-finger motifs crucial for t... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5h7r | ||||||
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Title | Structural basis of the flanking zinc-finger motifs crucial for the E3 ligase activity of the LNX1 RING domain | ||||||
Components | E3 ubiquitin-protein ligase LNX | ||||||
Keywords | LIGASE / RING / Ubiquitination / E3 ligase / Zn finger motif | ||||||
Function / homology | Function and homology information PDZ domain binding / RING-type E3 ubiquitin transferase / ubiquitin-protein transferase activity / Antigen processing: Ubiquitination & Proteasome degradation / ubiquitin-dependent protein catabolic process / protein ubiquitination / identical protein binding / metal ion binding / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å | ||||||
Authors | Nayak, D. / Sivaraman, J. | ||||||
Funding support | Singapore, 1items
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Citation | Journal: J. Mol. Biol. / Year: 2018 Title: Structure of LNX1:Ubc13~Ubiquitin Complex Reveals the Role of Additional Motifs for the E3 Ligase Activity of LNX1. Authors: Nayak, D. / Sivaraman, J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5h7r.cif.gz | 69.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5h7r.ent.gz | 50.3 KB | Display | PDB format |
PDBx/mmJSON format | 5h7r.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/h7/5h7r ftp://data.pdbj.org/pub/pdb/validation_reports/h7/5h7r | HTTPS FTP |
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-Related structure data
Related structure data | 5h7sC 5dinS C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 14625.937 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 11-138 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: LNX1, LNX, PDZRN2, UNQ574/PRO1136 / Production host: Escherichia coli (E. coli) References: UniProt: Q8TBB1, Ligases; Forming carbon-nitrogen bonds; Acid-amino-acid ligases (peptide synthases) | ||
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#2: Chemical | ChemComp-ZN / #3: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.53 Å3/Da / Density % sol: 65.12 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6 Details: 0.1 M MES monohydrate pH 6.0, 0.05 M calcium chloride dihydrate, 45 % polyethylene glycol 200 |
-Data collection
Diffraction | Mean temperature: 110 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.987 Å |
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jul 19, 2016 |
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.987 Å / Relative weight: 1 |
Reflection | Resolution: 1.51→79.884 Å / Num. obs: 31064 / % possible obs: 99.1 % / Redundancy: 17.6 % / Net I/σ(I): 19.8 |
Reflection shell | Resolution: 1.51→1.54 Å |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5DIN Resolution: 1.7→79.884 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.948 / SU B: 5.02 / SU ML: 0.07 / Cross valid method: THROUGHOUT / ESU R: 0.094 / ESU R Free: 0.084 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.7 Å / Shrinkage radii: 0.7 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 29.799 Å2
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Refinement step | Cycle: 1 / Resolution: 1.7→79.884 Å
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Refine LS restraints |
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