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Yorodumi- PDB-6les: 3D domain-swapped dimer of the maltose-binding protein fused to a... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6les | ||||||
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Title | 3D domain-swapped dimer of the maltose-binding protein fused to a fragment of the focal adhesion kinase | ||||||
Components | Maltose/maltodextrin-binding periplasmic protein,Focal adhesion kinase 1 | ||||||
Keywords | SUGAR BINDING PROTEIN / maltose binding protein / domain-swapping / arm exchange / folding / passenger protein / surface entropy reduction / fixed-arm carrier / dimer / FAK / apo-protein | ||||||
Function / homology | Function and homology information netrin-activated signaling pathway / regulation of substrate adhesion-dependent cell spreading / regulation of endothelial cell migration / regulation of epithelial cell migration / detection of muscle stretch / positive regulation of ubiquitin-dependent protein catabolic process / JUN kinase binding / signal complex assembly / positive regulation of macrophage proliferation / positive regulation of fibroblast migration ...netrin-activated signaling pathway / regulation of substrate adhesion-dependent cell spreading / regulation of endothelial cell migration / regulation of epithelial cell migration / detection of muscle stretch / positive regulation of ubiquitin-dependent protein catabolic process / JUN kinase binding / signal complex assembly / positive regulation of macrophage proliferation / positive regulation of fibroblast migration / DCC mediated attractive signaling / Signal regulatory protein family interactions / growth hormone receptor signaling pathway / regulation of osteoblast differentiation / regulation of cytoskeleton organization / MET activates PTK2 signaling / regulation of focal adhesion assembly / establishment of cell polarity / positive regulation of wound healing / positive regulation of macrophage chemotaxis / detection of maltose stimulus / regulation of GTPase activity / maltose binding / Fc-gamma receptor signaling pathway involved in phagocytosis / maltose transport complex / p130Cas linkage to MAPK signaling for integrins / positive regulation of epithelial cell migration / maltose transport / negative regulation of cell-cell adhesion / maltodextrin transmembrane transport / Apoptotic cleavage of cellular proteins / regulation of cell adhesion mediated by integrin / GRB2:SOS provides linkage to MAPK signaling for Integrins / carbohydrate transmembrane transporter activity / ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing / negative regulation of anoikis / carbohydrate transport / Estrogen-dependent nuclear events downstream of ESR-membrane signaling / RHO GTPases Activate WASPs and WAVEs / positive regulation of epithelial to mesenchymal transition / ephrin receptor signaling pathway / positive regulation of protein kinase activity / vascular endothelial growth factor receptor signaling pathway / regulation of cell adhesion / heart morphogenesis / stress fiber / EPHB-mediated forward signaling / SH2 domain binding / NCAM signaling for neurite out-growth / ATP-binding cassette (ABC) transporter complex / cell chemotaxis / Integrin signaling / transforming growth factor beta receptor signaling pathway / ciliary basal body / placenta development / protein tyrosine phosphatase activity / cell motility / molecular function activator activity / integrin-mediated signaling pathway / axon guidance / FCGR3A-mediated phagocytosis / regulation of protein phosphorylation / non-specific protein-tyrosine kinase / non-membrane spanning protein tyrosine kinase activity / epidermal growth factor receptor signaling pathway / Regulation of actin dynamics for phagocytic cup formation / VEGFA-VEGFR2 Pathway / peptidyl-tyrosine phosphorylation / cell migration / integrin binding / outer membrane-bounded periplasmic space / actin binding / regulation of cell population proliferation / cell cortex / regulation of cell shape / RAF/MAP kinase cascade / protein phosphatase binding / angiogenesis / protein tyrosine kinase activity / dendritic spine / Extra-nuclear estrogen signaling / protein autophosphorylation / periplasmic space / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / cytoskeleton / positive regulation of cell migration / positive regulation of protein phosphorylation / focal adhesion / intracellular membrane-bounded organelle / centrosome / DNA damage response / positive regulation of cell population proliferation / negative regulation of apoptotic process / protein kinase binding / perinuclear region of cytoplasm / ATP binding / membrane / nucleus / plasma membrane / cytosol Similarity search - Function | ||||||
Biological species | Escherichia coli (E. coli) Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.004 Å | ||||||
Authors | Momin, A.A. / Shahul Hameed, U.F. / Arold, S.T. | ||||||
Funding support | Saudi Arabia, 1items
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Citation | Journal: Sci Rep / Year: 2019 Title: Passenger sequences can promote interlaced dimers in a common variant of the maltose-binding protein. Authors: Momin, A.A. / Hameed, U.F.S. / Arold, S.T. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6les.cif.gz | 575 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6les.ent.gz | 476.5 KB | Display | PDB format |
PDBx/mmJSON format | 6les.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/le/6les ftp://data.pdbj.org/pub/pdb/validation_reports/le/6les | HTTPS FTP |
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-Related structure data
Related structure data | 6lf3C 5bmyS C: citing same article (ref.) S: Starting model for refinement |
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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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-Components
#1: Protein | Mass: 43853.605 Da / Num. of mol.: 4 Mutation: surface entropy reduction mutant,D83A,K84A,E173A,N174A,K240A,E360A,K363A,D364A Source method: isolated from a genetically manipulated source Details: residues 805-832 of the human focal adhesion kinase are C-terminally fused to the maltose-binding protein Source: (gene. exp.) Escherichia coli (strain K12) (bacteria), (gene. exp.) Homo sapiens (human) Gene: malE, b4034, JW3994, PTK2, FAK, FAK1 / Plasmid: pJEx411c / Production host: Escherichia coli BL21(DE3) (bacteria) References: UniProt: P0AEX9, UniProt: Q05397, non-specific protein-tyrosine kinase #2: Chemical | #3: 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: 2.35 Å3/Da / Density % sol: 42.5 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 10.5 Details: 2000mM Ammonium sulfate, 100mM CAPS/ Sodium hydroxide pH 10.5 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 2 / Wavelength: 0.98 Å |
Detector | Type: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Jul 13, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 |
Reflection | Resolution: 2→47.49 Å / Num. obs: 93102 / % possible obs: 95.33 % / Redundancy: 8.12 % / Biso Wilson estimate: 46.1 Å2 / CC1/2: 0.995 / Rmerge(I) obs: 0.1033 / Rpim(I) all: 0.06574 / Rrim(I) all: 0.1229 / Χ2: 0.86 / Net I/σ(I): 8.07 |
Reflection shell | Resolution: 2.004→2.076 Å / Redundancy: 1.2 % / Rmerge(I) obs: 0.944 / Mean I/σ(I) obs: 1.2 / Num. unique obs: 8178 / CC1/2: 0.6 / Rpim(I) all: 0.7233 / Χ2: 0.55 / % possible all: 84.49 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5BMY Resolution: 2.004→47.45 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.951 / SU B: 13.811 / SU ML: 0.175 / Cross valid method: THROUGHOUT / ESU R: 0.221 / ESU R Free: 0.174 Details: U VALUES : WITH TLS ADDED HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : RESIDUAL ONLY
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Solvent computation | Ion probe radii: 0.7 Å / Shrinkage radii: 0.7 Å / VDW probe radii: 1.1 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 129.9 Å2 / Biso mean: 50.329 Å2 / Biso min: 26.93 Å2
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Refinement step | Cycle: final / Resolution: 2.004→47.45 Å
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LS refinement shell | Resolution: 2.004→2.056 Å / Rfactor Rfree error: 0
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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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