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Yorodumi- PDB-6tg8: Crystal structure of the Kelch domain in complex with 11 amino ac... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6tg8 | ||||||
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Title | Crystal structure of the Kelch domain in complex with 11 amino acid peptide (model of the ETGE loop) | ||||||
Components |
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Keywords | LIGASE / complex / beta proteins / Kelch motif | ||||||
Function / homology | Function and homology information regulation of epidermal cell differentiation / negative regulation of response to oxidative stress / Nuclear events mediated by NFE2L2 / Cul3-RING ubiquitin ligase complex / centriolar satellite / ubiquitin-like ligase-substrate adaptor activity / cellular response to interleukin-4 / inclusion body / regulation of autophagy / actin filament ...regulation of epidermal cell differentiation / negative regulation of response to oxidative stress / Nuclear events mediated by NFE2L2 / Cul3-RING ubiquitin ligase complex / centriolar satellite / ubiquitin-like ligase-substrate adaptor activity / cellular response to interleukin-4 / inclusion body / regulation of autophagy / actin filament / negative regulation of DNA-binding transcription factor activity / disordered domain specific binding / KEAP1-NFE2L2 pathway / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / Antigen processing: Ubiquitination & Proteasome degradation / Neddylation / cellular response to oxidative stress / midbody / ubiquitin-dependent protein catabolic process / Potential therapeutics for SARS / in utero embryonic development / RNA polymerase II-specific DNA-binding transcription factor binding / Ub-specific processing proteases / protein ubiquitination / endoplasmic reticulum / nucleoplasm / identical protein binding / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.75 Å | ||||||
Authors | Kekez, I. / Matic, S. / Tomic, S. / Matkovic-Calogovic, D. | ||||||
Funding support | Croatia, 1items
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Citation | Journal: J.Biomol.Struct.Dyn. / Year: 2021 Title: Binding of dipeptidyl peptidase III to the oxidative stress cell sensor Kelch-like ECH-associated protein 1 is a two-step process. Authors: Matic, S. / Kekez, I. / Tomin, M. / Bogar, F. / Supljika, F. / Kazazic, S. / Hanic, M. / Jha, S. / Brkic, H. / Bourgeois, B. / Madl, T. / Gruber, K. / Macheroux, P. / Matkovic-Calogovic, D. ...Authors: Matic, S. / Kekez, I. / Tomin, M. / Bogar, F. / Supljika, F. / Kazazic, S. / Hanic, M. / Jha, S. / Brkic, H. / Bourgeois, B. / Madl, T. / Gruber, K. / Macheroux, P. / Matkovic-Calogovic, D. / Matovina, M. / Tomic, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6tg8.cif.gz | 75.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6tg8.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 6tg8.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6tg8_validation.pdf.gz | 676.4 KB | Display | wwPDB validaton report |
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Full document | 6tg8_full_validation.pdf.gz | 679 KB | Display | |
Data in XML | 6tg8_validation.xml.gz | 12.7 KB | Display | |
Data in CIF | 6tg8_validation.cif.gz | 16.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/tg/6tg8 ftp://data.pdbj.org/pub/pdb/validation_reports/tg/6tg8 | HTTPS FTP |
-Related structure data
Related structure data | 1zgkS 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: 31583.299 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: KEAP1, INRF2, KIAA0132, KLHL19 / Production host: Escherichia coli (E. coli) / References: UniProt: Q14145 |
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#2: Protein/peptide | Mass: 1227.320 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) |
#3: Chemical | ChemComp-NA / |
#4: Water | ChemComp-HOH / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.18 Å3/Da / Density % sol: 61.33 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7 Details: 1.8 M sodium acetate pH 7.0, 0.1 M Bis-Tris propane pH 7.0 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: ELETTRA / Beamline: 5.2R / Wavelength: 1 Å |
Detector | Type: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Oct 4, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.45→65.208 Å / Num. obs: 11948 / % possible obs: 99.5 % / Redundancy: 18.1 % / Rmerge(I) obs: 0.11 / Net I/σ(I): 40.66 |
Reflection shell | Resolution: 2.7→2.8 Å / Rmerge(I) obs: 0.614 / Num. unique obs: 1198 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1zgk Resolution: 2.75→17 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.923 / SU B: 18.237 / SU ML: 0.321 / Cross valid method: FREE R-VALUE / ESU R: 0.651 / ESU R Free: 0.337 Details: Hydrogens have been added in their 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 69.133 Å2
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Refinement step | Cycle: LAST / Resolution: 2.75→17 Å
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Refine LS restraints |
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LS refinement shell |
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