+Open data
-Basic information
Entry | Database: PDB / ID: 3ii7 | ||||||
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Title | Crystal structure of the kelch domain of human KLHL7 | ||||||
Components | Kelch-like protein 7 | ||||||
Keywords | PROTEIN BINDING / Protein-binding / kelch-repeat / Structural Genomics / Structural Genomics Consortium / SGC / Kelch repeat / Nucleus | ||||||
Function / homology | Function and homology information Cul3-RING ubiquitin ligase complex / protein ubiquitination / nucleolus / perinuclear region of cytoplasm / protein homodimerization activity / nucleoplasm / identical protein binding / plasma membrane / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.63 Å | ||||||
Authors | Chaikuad, A. / Thangaratnarajah, C. / Cooper, C.D.O. / Ugochukwu, E. / Muniz, J.R.C. / Krojer, T. / Sethi, R. / Pike, A.C.W. / Filippakopoulos, P. / von Delft, F. ...Chaikuad, A. / Thangaratnarajah, C. / Cooper, C.D.O. / Ugochukwu, E. / Muniz, J.R.C. / Krojer, T. / Sethi, R. / Pike, A.C.W. / Filippakopoulos, P. / von Delft, F. / Arrowsmith, C.H. / Edwards, A.M. / Weigelt, J. / Bountra, C. / Knapp, S. / Bullock, A. / Structural Genomics Consortium (SGC) | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2013 Title: Structural basis for Cul3 protein assembly with the BTB-Kelch family of E3 ubiquitin ligases. Authors: Canning, P. / Cooper, C.D. / Krojer, T. / Murray, J.W. / Pike, A.C. / Chaikuad, A. / Keates, T. / Thangaratnarajah, C. / Hojzan, V. / Ayinampudi, V. / Marsden, B.D. / Gileadi, O. / Knapp, S. ...Authors: Canning, P. / Cooper, C.D. / Krojer, T. / Murray, J.W. / Pike, A.C. / Chaikuad, A. / Keates, T. / Thangaratnarajah, C. / Hojzan, V. / Ayinampudi, V. / Marsden, B.D. / Gileadi, O. / Knapp, S. / von Delft, F. / Bullock, A.N. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3ii7.cif.gz | 84.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3ii7.ent.gz | 62 KB | Display | PDB format |
PDBx/mmJSON format | 3ii7.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3ii7_validation.pdf.gz | 445.4 KB | Display | wwPDB validaton report |
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Full document | 3ii7_full_validation.pdf.gz | 446.9 KB | Display | |
Data in XML | 3ii7_validation.xml.gz | 16.8 KB | Display | |
Data in CIF | 3ii7_validation.cif.gz | 25.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ii/3ii7 ftp://data.pdbj.org/pub/pdb/validation_reports/ii/3ii7 | HTTPS FTP |
-Related structure data
Related structure data | 2vpjSC 2xn4C 4ap2C 4apfC 4ascC S: Starting model for refinement C: citing same article (ref.) |
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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 on special symmetry positions |
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-Components
#1: Protein | Mass: 34074.789 Da / Num. of mol.: 1 / Fragment: Kelch-repeat domain, UNP residues 283-586 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: KLHL7 / Plasmid: pNIC28-BSA4 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)-R3-pRARE2 / References: UniProt: Q8IXQ5 | ||
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#2: Chemical | ChemComp-EDO / #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: 2.3 Å3/Da / Density % sol: 46.43 % |
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Crystal grow | Temperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: 12% PEG 20000, 0.1M MES pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 293.15K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU FR-E SUPERBRIGHT / Wavelength: 1.5418 Å |
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Jun 25, 2009 |
Radiation | Monochromator: Flat graphite crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.63→28.34 Å / Num. all: 38411 / Num. obs: 38407 / % possible obs: 99.2 % / Observed criterion σ(I): 2 / Redundancy: 6.5 % / Biso Wilson estimate: 17.4 Å2 / Rmerge(I) obs: 0.083 / Net I/σ(I): 13.8 |
Reflection shell | Resolution: 1.63→1.72 Å / Redundancy: 6 % / Rmerge(I) obs: 0.636 / Mean I/σ(I) obs: 2.6 / Num. unique all: 5515 / % possible all: 98.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 2VPJ Resolution: 1.63→28.34 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.951 / SU B: 3.177 / SU ML: 0.05 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 2 / ESU R: 0.088 / ESU R Free: 0.087 / 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: 8.797 Å2
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Refine analyze | Luzzati coordinate error obs: 0.176 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.63→28.34 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.63→1.672 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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