+Open data
-Basic information
Entry | Database: PDB / ID: 7kk7 | |||||||||
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Title | crystal structure of ligand-free PLEKHA7 PH domain | |||||||||
Components | Pleckstrin homology domain-containing family A member 7 | |||||||||
Keywords | CELL ADHESION / PLEKHA7 / PH domain / Pleckstrin homology domain / PIP / inositol-phosphate | |||||||||
Function / homology | Function and homology information zonula adherens maintenance / epithelial cell-cell adhesion / zonula adherens / pore complex assembly / delta-catenin binding / cell-cell adhesion mediated by cadherin / pore complex / cell junction / centrosome / extracellular exosome ...zonula adherens maintenance / epithelial cell-cell adhesion / zonula adherens / pore complex assembly / delta-catenin binding / cell-cell adhesion mediated by cadherin / pore complex / cell junction / centrosome / extracellular exosome / nucleoplasm / cytosol Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å | |||||||||
Authors | Marassi, F.M. / Aleshin, A.E. / Liddington, R.C. | |||||||||
Funding support | United States, 2items
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Citation | Journal: Structure / Year: 2021 Title: Structural basis for the association of PLEKHA7 with membrane-embedded phosphatidylinositol lipids. Authors: Aleshin, A.E. / Yao, Y. / Iftikhar, A. / Bobkov, A.A. / Yu, J. / Cadwell, G. / Klein, M.G. / Dong, C. / Bankston, L.A. / Liddington, R.C. / Im, W. / Powis, G. / Marassi, F.M. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7kk7.cif.gz | 103.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7kk7.ent.gz | 78.3 KB | Display | PDB format |
PDBx/mmJSON format | 7kk7.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/kk/7kk7 ftp://data.pdbj.org/pub/pdb/validation_reports/kk/7kk7 | HTTPS FTP |
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-Related structure data
Related structure data | 7kjoSC 7kjzC 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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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: 0 / Ens-ID: 1 / Beg auth comp-ID: SER / Beg label comp-ID: SER / End auth comp-ID: GLN / End label comp-ID: GLN / Refine code: 0 / Auth seq-ID: 163 - 282 / Label seq-ID: 5 - 124
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-Components
#1: Protein | Mass: 14422.345 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: PLEKHA7 / Production host: Escherichia coli (E. coli) / References: UniProt: Q6IQ23 #2: Chemical | #3: Chemical | ChemComp-EDO / | #4: Water | ChemComp-HOH / | Has ligand of interest | N | |
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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: 2.3 Å3/Da / Density % sol: 46.57 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7 Details: Protein in 180 mM NaCl, 20 mM Tris pH 8, 50 mM BisTris pH 6.0, 0.7 mM TCEP was mixed with 20% PEG 3350, 0.02 mM MgCl2, 100 mM HEPES pH 7.0 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.1158 Å |
Detector | Type: DECTRIS PILATUS 300K / Detector: PIXEL / Date: Nov 4, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.1158 Å / Relative weight: 1 |
Reflection | Resolution: 2.8→47.2 Å / Num. obs: 6980 / % possible obs: 100 % / Redundancy: 6.8 % / Rmerge(I) obs: 0.071 / Net I/σ(I): 16 |
Reflection shell | Resolution: 2.8→2.95 Å / Redundancy: 7.1 % / Rmerge(I) obs: 0.81 / Num. unique obs: 1000 / CC1/2: 0.89 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 7KJO Resolution: 2.8→47.19 Å / Cor.coef. Fo:Fc: 0.94 / Cor.coef. Fo:Fc free: 0.915 / SU B: 37.113 / SU ML: 0.32 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.405 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 241.57 Å2 / Biso mean: 93.507 Å2 / Biso min: 30 Å2
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Refinement step | Cycle: final / Resolution: 2.8→47.19 Å
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Refine LS restraints |
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Refine LS restraints NCS | Ens-ID: 1 / Number: 2880 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.17 Å / Weight position: 0.05
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LS refinement shell | Resolution: 2.8→2.873 Å / Rfactor Rfree error: 0 / 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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