+Open data
-Basic information
Entry | Database: PDB / ID: 4uij | |||||||||
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Title | Crystal structure of the BTB domain of KCTD13 | |||||||||
Components | BTB/POZ DOMAIN-CONTAINING ADAPTER FOR CUL3-MEDIATED RHOA DEGRADATION PROTEIN 1 | |||||||||
Keywords | SIGNALING PROTEIN | |||||||||
Function / homology | Function and homology information small GTPase binding => GO:0031267 / negative regulation of Rho protein signal transduction / Cul3-RING ubiquitin ligase complex / stress fiber assembly / positive regulation of synaptic transmission / positive regulation of DNA replication / protein homooligomerization / cell migration / proteasome-mediated ubiquitin-dependent protein catabolic process / DNA replication ...small GTPase binding => GO:0031267 / negative regulation of Rho protein signal transduction / Cul3-RING ubiquitin ligase complex / stress fiber assembly / positive regulation of synaptic transmission / positive regulation of DNA replication / protein homooligomerization / cell migration / proteasome-mediated ubiquitin-dependent protein catabolic process / DNA replication / protein ubiquitination / nuclear body / protein domain specific binding / nucleoplasm / identical protein binding Similarity search - Function | |||||||||
Biological species | HOMO SAPIENS (human) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å | |||||||||
Authors | Pinkas, D.M. / Sanvitale, C.E. / Sorell, F.J. / Solcan, N. / Goubin, S. / Canning, P. / Williams, E. / Chaikuad, A. / Dixon Clarke, S.E. / Tallant, C. ...Pinkas, D.M. / Sanvitale, C.E. / Sorell, F.J. / Solcan, N. / Goubin, S. / Canning, P. / Williams, E. / Chaikuad, A. / Dixon Clarke, S.E. / Tallant, C. / Fonseca, M. / Chalk, R. / Doutch, J. / Krojer, T. / Burgess-Brown, N.A. / von Delft, F. / Arrowsmith, C.H. / Edwards, A.M. / Bountra, C. / Bullock, A. | |||||||||
Citation | Journal: Biochem. J. / Year: 2017 Title: Structural complexity in the KCTD family of Cullin3-dependent E3 ubiquitin ligases. Authors: Pinkas, D.M. / Sanvitale, C.E. / Bufton, J.C. / Sorrell, F.J. / Solcan, N. / Chalk, R. / Doutch, J. / 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 | 4uij.cif.gz | 159.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4uij.ent.gz | 126.8 KB | Display | PDB format |
PDBx/mmJSON format | 4uij.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ui/4uij ftp://data.pdbj.org/pub/pdb/validation_reports/ui/4uij | HTTPS FTP |
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-Related structure data
Related structure data | 4crhC 5a15C 5a6rC 5ftaC 4ues 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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2 |
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3 |
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4 |
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Unit cell |
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-Components
#1: Protein | Mass: 15715.845 Da / Num. of mol.: 4 / Fragment: BTB DOMAIN, UNP RESIDUES 27-144 Source method: isolated from a genetically manipulated source Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / References: UniProt: Q8WZ19 #2: Chemical | ChemComp-CL / #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 1.94 Å3/Da / Density % sol: 36.74 % / Description: NONE |
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Crystal grow | pH: 6.5 / Details: 1.6M MAGNESIUM SULFATE, 0.1M MES PH 6.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.97625 |
Detector | Type: DECTRIS PIXEL / Detector: PIXEL / Date: May 23, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97625 Å / Relative weight: 1 |
Reflection | Resolution: 2.7→37.42 Å / Num. obs: 13431 / % possible obs: 99.8 % / Observed criterion σ(I): -1 / Redundancy: 5 % / Biso Wilson estimate: 57.35 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 8.3 |
Reflection shell | Resolution: 2.7→2.83 Å / Redundancy: 5 % / Mean I/σ(I) obs: 2 / % possible all: 99.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 4UES 4ues Resolution: 2.7→37.417 Å / SU ML: 0.39 / σ(F): 1.35 / Phase error: 29.22 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.7→37.417 Å
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Refine LS restraints |
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LS refinement shell |
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