+Open data
-Basic information
Entry | Database: PDB / ID: 6fb4 | |||||||||
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Title | human KIBRA C2 domain mutant C771A | |||||||||
Components | Protein KIBRA | |||||||||
Keywords | LIPID BINDING PROTEIN / C2 domain / Kibra / phosphoinositide-binding / membrane interaction | |||||||||
Function / homology | Function and homology information regulation of intracellular transport / regulation of hippo signaling / negative regulation of organ growth / hippo signaling / Signaling by Hippo / NOTCH3 Intracellular Domain Regulates Transcription / establishment of cell polarity / negative regulation of hippo signaling / signaling adaptor activity / kinase binding ...regulation of intracellular transport / regulation of hippo signaling / negative regulation of organ growth / hippo signaling / Signaling by Hippo / NOTCH3 Intracellular Domain Regulates Transcription / establishment of cell polarity / negative regulation of hippo signaling / signaling adaptor activity / kinase binding / ruffle membrane / cell migration / transcription coactivator activity / positive regulation of MAPK cascade / molecular adaptor activity / negative regulation of cell population proliferation / regulation of DNA-templated transcription / perinuclear region of cytoplasm / negative regulation of transcription by RNA polymerase II / protein-containing complex / nucleus / cytoplasm / cytosol Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.4156309909 Å | |||||||||
Authors | Crennell, S.J. / Posner, M.G. / Bagby, S. | |||||||||
Funding support | United Kingdom, 1items
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Citation | Journal: J. Biol. Chem. / Year: 2018 Title: Distinctive phosphoinositide- and Ca2+-binding properties of normal and cognitive performance-linked variant forms of KIBRA C2 domain. Authors: Posner, M.G. / Upadhyay, A. / Ishima, R. / Kalli, A.C. / Harris, G. / Kremerskothen, J. / Sansom, M.S.P. / Crennell, S.J. / Bagby, S. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6fb4.cif.gz | 137 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6fb4.ent.gz | 89.2 KB | Display | PDB format |
PDBx/mmJSON format | 6fb4.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fb/6fb4 ftp://data.pdbj.org/pub/pdb/validation_reports/fb/6fb4 | HTTPS FTP |
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-Related structure data
Related structure data | 6fd0C 6fjcC 6fjdC 3k9dS 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: 14547.594 Da / Num. of mol.: 2 / Mutation: C771A Source method: isolated from a genetically manipulated source Details: KIBRA is a multi-functional scaffold protein, the C2 domain binds phosphoinositides. Source: (gene. exp.) Homo sapiens (human) / Gene: WWC1, KIAA0869 / Organ: kidney, brain / Plasmid: pQE30 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q8IX03 #2: Chemical | ChemComp-GOL / #3: Chemical | ChemComp-PO4 / | #4: 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: 3.63 Å3/Da / Density % sol: 66.08 % / Description: pavilion |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 0.1M Na HEPES, 0.8M Na dihydrogen phosphare, 0.8M K dihydrogen phosphate 5% glycerol cryoprotectant |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54 Å |
Detector | Type: RIGAKU SATURN 944+ / Detector: CCD / Date: Sep 3, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54 Å / Relative weight: 1 |
Reflection | Resolution: 2.415→72.643 Å / Num. obs: 17355 / % possible obs: 99.9 % / Redundancy: 10.6 % / Biso Wilson estimate: 41.2630665184 Å2 / Rmerge(I) obs: 0.133 / Rrim(I) all: 0.14 / Χ2: 0.96 / Net I/σ(I): 10.7 |
Reflection shell | Resolution: 2.42→2.5 Å / Redundancy: 6.22 % / Rmerge(I) obs: 0.625 / Mean I/σ(I) obs: 1.7 / Rrim(I) all: 0.676 / Χ2: 1.34 / % possible all: 98.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3K9D Resolution: 2.4156309909→72.6422108694 Å / SU ML: 0.325016801318 / Cross valid method: FREE R-VALUE / σ(F): 1.35109357799 / Phase error: 25.3297439476 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 55.639236193 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.4156309909→72.6422108694 Å
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Refine LS restraints |
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LS refinement shell |
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