+Open data
-Basic information
Entry | Database: PDB / ID: 6g57 | ||||||
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Title | Structure of the H1 domain of human KCTD8 | ||||||
Components | BTB/POZ domain-containing protein KCTD8 | ||||||
Keywords | LIGASE / KCTD8 / C-terminal Domain / H1 domain | ||||||
Function / homology | Function and homology information regulation of G protein-coupled receptor signaling pathway / cell projection / protein homooligomerization / presynaptic membrane / postsynaptic membrane / receptor complex Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å | ||||||
Authors | Pinkas, D.M. / Bufton, J.C. / Strain-Damerell, C.M. / Fairhead, M. / Burgess-Brown, N.A. / von Delft, F. / Arrowsmith, C.H. / Edwards, A.M. / Bountra, C. / Bullock, A.N. | ||||||
Citation | Journal: To Be Published Title: Structure of the H1 domain of human KCTD8 Authors: Pinkas, D.M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6g57.cif.gz | 144.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6g57.ent.gz | 113.5 KB | Display | PDB format |
PDBx/mmJSON format | 6g57.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/g5/6g57 ftp://data.pdbj.org/pub/pdb/validation_reports/g5/6g57 | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 14437.193 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: KCTD8 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Rosetta / References: UniProt: Q6ZWB6 #2: 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: 2.33 Å3/Da / Density % sol: 47.12 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop Details: 50% PEG200 -- 0.2M sodium chloride -- 0.1M sodium/potassium phosphate pH 7.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.9159 Å |
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jul 17, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9159 Å / Relative weight: 1 |
Reflection | Resolution: 2.75→79.79 Å / Num. obs: 15121 / % possible obs: 100 % / Redundancy: 18.5 % / Net I/σ(I): 16.1 |
Reflection shell | Resolution: 2.75→2.82 Å / Redundancy: 18.1 % / Num. unique obs: 1070 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: Human KCTD16 H1 (unpublished) Resolution: 2.8→79.775 Å / SU ML: 0.46 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 35.39
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.8→79.775 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Origin x: 43.4722 Å / Origin y: 52.63 Å / Origin z: 93.8565 Å
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Refinement TLS group | Selection details: all |