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Yorodumi- PDB-4ifn: Crystal Structures of apo Keap1, Keap1-peptide, and Keap1-compoun... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4ifn | ||||||
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Title | Crystal Structures of apo Keap1, Keap1-peptide, and Keap1-compound complexes | ||||||
Components | kelch-like ECH-associated protein 1 | ||||||
Keywords | TRANSCRIPTION / PROTEIN BINDING | ||||||
Function / homology | Function and homology information negative regulation of response to oxidative stress / regulation of epidermal cell differentiation / 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 response to oxidative stress / regulation of epidermal cell differentiation / 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 / KEAP1-NFE2L2 pathway / disordered domain specific binding / 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 / 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 / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.4 Å | ||||||
Authors | Pan, H. / Lin, M. / Yang, Y. / Callaway, K. / Baker, J. / Diep, L. / Yan, J. / Tanaka, K. / Zhu, Y.L. / Konradi, A.W. ...Pan, H. / Lin, M. / Yang, Y. / Callaway, K. / Baker, J. / Diep, L. / Yan, J. / Tanaka, K. / Zhu, Y.L. / Konradi, A.W. / Jobling, M. / Tam, D. / Ren, Z. / Cheung, H. / Bova, M. / Riley, B.E. / Yao, N. / Artis, D.R. | ||||||
Citation | Journal: Acta Crystallogr.,Sect.D Title: Crystal Structures of apo Keap1, Keap1-peptide, and Keap1-compound complexes Authors: Pan, H. / Lin, M. / Yang, Y. / Callaway, K. / Baker, J. / Diep, L. / Yan, J. / Tanaka, K. / Zhu, Y.L. / Konradi, A.W. / Jobling, M. / Tam, D. / Ren, Z. / Cheung, H. / Bova, M. / Riley, B.E. ...Authors: Pan, H. / Lin, M. / Yang, Y. / Callaway, K. / Baker, J. / Diep, L. / Yan, J. / Tanaka, K. / Zhu, Y.L. / Konradi, A.W. / Jobling, M. / Tam, D. / Ren, Z. / Cheung, H. / Bova, M. / Riley, B.E. / Yao, N. / Artis, D.R. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4ifn.cif.gz | 66.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4ifn.ent.gz | 53 KB | Display | PDB format |
PDBx/mmJSON format | 4ifn.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/if/4ifn ftp://data.pdbj.org/pub/pdb/validation_reports/if/4ifn | HTTPS FTP |
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-Related 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: 31828.525 Da / Num. of mol.: 1 / Fragment: Kelch domain, UNP residues 321-609 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: Chemical | ChemComp-12O / ( |
#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: 3.45 Å3/Da / Density % sol: 64.38 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 8.1 Details: 0.6 M Sodium Formate, 0.2 M Ammonium Acetate, 0.1 M Tris pH 8.1, VAPOR DIFFUSION, SITTING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 180 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å |
Detector | Type: RIGAKU RAXIS HTC / Detector: IMAGE PLATE / Date: Aug 30, 2012 |
Radiation | Monochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.4→35.28 Å / Num. all: 15724 / Num. obs: 15676 / % possible obs: 96.69 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 |
Reflection shell | Resolution: 2.4→2.462 Å / % possible all: 99.37 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.4→35.28 Å / Cor.coef. Fo:Fc: 0.902 / Cor.coef. Fo:Fc free: 0.819 / SU B: 13.232 / SU ML: 0.301 / Cross valid method: THROUGHOUT / ESU R: 0.412 / ESU R Free: 0.356 / 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: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 33.217 Å2
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Refinement step | Cycle: LAST / Resolution: 2.4→35.28 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.4→2.462 Å / Total num. of bins used: 20
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