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Open data
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Basic information
Entry | Database: PDB / ID: 1zgk | ||||||
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Title | 1.35 angstrom structure of the Kelch domain of Keap1 | ||||||
![]() | Kelch-like ECH-associated protein 1 | ||||||
![]() | PROTEIN BINDING / BETA-PROPELLER / KELCH REPEAT MOTIF | ||||||
Function / homology | ![]() regulation of epidermal cell differentiation / negative regulation of response to oxidative stress / Nuclear events mediated by NFE2L2 / Cul3-RING ubiquitin ligase complex / ubiquitin-like ligase-substrate adaptor activity / centriolar satellite / 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 / ubiquitin-like ligase-substrate adaptor activity / centriolar satellite / cellular response to interleukin-4 / inclusion body / regulation of autophagy / actin filament / negative regulation of DNA-binding transcription factor activity / KEAP1-NFE2L2 pathway / disordered domain specific binding / Antigen processing: Ubiquitination & Proteasome degradation / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / Neddylation / midbody / cellular response to oxidative stress / ubiquitin-dependent protein catabolic process / in utero embryonic development / RNA polymerase II-specific DNA-binding transcription factor binding / Potential therapeutics for SARS / Ub-specific processing proteases / protein ubiquitination / endoplasmic reticulum / nucleoplasm / identical protein binding / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Li, X. / Bottoms, C.A. / Hannink, M. / Beamer, L.J. | ||||||
![]() | ![]() Title: Conserved solvent and side-chain interactions in the 1.35 Angstrom structure of the Kelch domain of Keap1. Authors: Beamer, L.J. / Li, X. / Bottoms, C.A. / Hannink, M. #1: ![]() Title: Crystal structure of the Kelch domain of human Keap1 Authors: Li, X. / Zhang, D. / Hannink, M. / Beamer, L.J. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 135.4 KB | Display | ![]() |
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PDB format | ![]() | 111.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 359.9 KB | Display | ![]() |
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Full document | ![]() | 361.6 KB | Display | |
Data in XML | ![]() | 6.8 KB | Display | |
Data in CIF | ![]() | 12.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | |
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Similar 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: 34021.801 Da / Num. of mol.: 1 / Fragment: KELCH domain Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.6 Å3/Da / Density % sol: 52.6 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 4% PEG 4000, 100 MM NA HEPES, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 1.35→50 Å / Num. all: 71295 / Num. obs: 71295 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 17.5 % / Rmerge(I) obs: 0.079 / Net I/σ(I): 86.8 |
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Processing
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Refinement | Method to determine structure: ![]()
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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: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 9.032 Å2
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Refinement step | Cycle: LAST / Resolution: 1.35→28.06 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.35→1.385 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Origin x: 1.9293 Å / Origin y: 31.5486 Å / Origin z: 68.5818 Å
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