+Open data
-Basic information
Entry | Database: PDB / ID: 1zgk | ||||||
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Title | 1.35 angstrom structure of the Kelch domain of Keap1 | ||||||
Components | Kelch-like ECH-associated protein 1 | ||||||
Keywords | PROTEIN BINDING / BETA-PROPELLER / KELCH REPEAT MOTIF | ||||||
Function / homology | Function and homology information regulation of epidermal cell differentiation / Nuclear events mediated by NFE2L2 / Cul3-RING ubiquitin ligase complex / ubiquitin-like ligase-substrate adaptor activity / centriolar satellite / inclusion body / cellular response to interleukin-4 / regulation of autophagy / actin filament / negative regulation of DNA-binding transcription factor activity ...regulation of epidermal cell differentiation / Nuclear events mediated by NFE2L2 / Cul3-RING ubiquitin ligase complex / ubiquitin-like ligase-substrate adaptor activity / centriolar satellite / inclusion body / cellular response to interleukin-4 / regulation of autophagy / actin filament / negative regulation of DNA-binding transcription factor activity / KEAP1-NFE2L2 pathway / disordered domain specific binding / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / Antigen processing: Ubiquitination & Proteasome degradation / cellular response to oxidative stress / Neddylation / midbody / ubiquitin-dependent protein catabolic process / in utero embryonic development / RNA polymerase II-specific DNA-binding transcription factor binding / Potential therapeutics for SARS / protein ubiquitination / Ub-specific processing proteases / endoplasmic reticulum / nucleoplasm / identical protein binding / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.35 Å | ||||||
Authors | Li, X. / Bottoms, C.A. / Hannink, M. / Beamer, L.J. | ||||||
Citation | Journal: Acta Crystallogr.,Sect.D / Year: 2005 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: Journal: J.Biol.Chem. / Year: 2004 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1zgk.cif.gz | 135.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1zgk.ent.gz | 111.7 KB | Display | PDB format |
PDBx/mmJSON format | 1zgk.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zg/1zgk ftp://data.pdbj.org/pub/pdb/validation_reports/zg/1zgk | HTTPS FTP |
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-Related structure data
Related structure data | |
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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: 34021.801 Da / Num. of mol.: 1 / Fragment: KELCH domain Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: KEAP1, KIAA0132 / Plasmid: PET15B / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)PLYSS / References: UniProt: Q14145 |
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#2: 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: 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: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.979 / Wavelength: 0.979 Å |
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 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 1.35→28.06 Å / Cor.coef. Fo:Fc: 0.98 / Cor.coef. Fo:Fc free: 0.974 / SU B: 1.008 / SU ML: 0.019 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.04 / ESU R Free: 0.038 / 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: 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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