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Yorodumi- PDB-3kzd: Crystal Structure of Free T-cell Lymphoma Invasion and Metastasis... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3kzd | ||||||
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Title | Crystal Structure of Free T-cell Lymphoma Invasion and Metastasis-1 PDZ Domain | ||||||
Components | T-lymphoma invasion and metastasis-inducing protein 1 | ||||||
Keywords | SIGNALING PROTEIN / PDZ / CELL JUNCTION / CELL ADHESION / TIAM1 / Guanine nucleotide exchange factor / Guanine-nucleotide releasing factor / Lipoprotein / Myristate / Phosphoprotein / Polymorphism | ||||||
Function / homology | Function and homology information positive regulation of Schwann cell chemotaxis / regulation of non-canonical Wnt signaling pathway / regulation of dopaminergic neuron differentiation / extrinsic component of postsynaptic density membrane / Activated NTRK2 signals through CDK5 / regulation of epithelial to mesenchymal transition / positive regulation of dendritic spine morphogenesis / regulation of insulin secretion involved in cellular response to glucose stimulus / regulation of modification of postsynaptic actin cytoskeleton / cell-cell contact zone ...positive regulation of Schwann cell chemotaxis / regulation of non-canonical Wnt signaling pathway / regulation of dopaminergic neuron differentiation / extrinsic component of postsynaptic density membrane / Activated NTRK2 signals through CDK5 / regulation of epithelial to mesenchymal transition / positive regulation of dendritic spine morphogenesis / regulation of insulin secretion involved in cellular response to glucose stimulus / regulation of modification of postsynaptic actin cytoskeleton / cell-cell contact zone / protein localization to membrane / cardiac muscle hypertrophy / activation of GTPase activity / regulation of small GTPase mediated signal transduction / Wnt signaling pathway, planar cell polarity pathway / main axon / neuron projection extension / positive regulation of axonogenesis / small GTPase-mediated signal transduction / NRAGE signals death through JNK / Rac protein signal transduction / CDC42 GTPase cycle / EPH-ephrin mediated repulsion of cells / RHOA GTPase cycle / RAC2 GTPase cycle / ephrin receptor signaling pathway / RAC3 GTPase cycle / axonal growth cone / positive regulation of epithelial to mesenchymal transition / RAC1 GTPase cycle / EPHB-mediated forward signaling / cell-matrix adhesion / guanyl-nucleotide exchange factor activity / regulation of ERK1 and ERK2 cascade / response to cocaine / receptor tyrosine kinase binding / kinase binding / ruffle membrane / G alpha (12/13) signalling events / cell-cell junction / cell migration / positive regulation of protein binding / microtubule binding / protein-containing complex assembly / microtubule / dendritic spine / positive regulation of cell migration / neuronal cell body / glutamatergic synapse / lipid binding / synapse / positive regulation of cell population proliferation / plasma membrane / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.3 Å | ||||||
Authors | Shepherd, T.R. / Fuentes, E.J. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2010 Title: The Tiam1 PDZ domain couples to Syndecan1 and promotes cell-matrix adhesion. Authors: Shepherd, T.R. / Klaus, S.M. / Liu, X. / Ramaswamy, S. / DeMali, K.A. / Fuentes, E.J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3kzd.cif.gz | 47.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3kzd.ent.gz | 33.4 KB | Display | PDB format |
PDBx/mmJSON format | 3kzd.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/kz/3kzd ftp://data.pdbj.org/pub/pdb/validation_reports/kz/3kzd | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 10154.440 Da / Num. of mol.: 1 / Fragment: PDZ Domain / Mutation: Q844H Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: TIAM1 / Plasmid: pET21a-6His-rTEV / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q13009 |
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#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.02 Å3/Da / Density % sol: 39.05 % |
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Crystal grow | Temperature: 288 K / Method: vapor diffusion, hanging drop / pH: 8 Details: 20% (w/v) PEG 3350, 0.2 M NaSCN, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 288K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.0332 Å |
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jun 16, 2007 |
Radiation | Monochromator: Double crystal cryo-cooled Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.0332 Å / Relative weight: 1 |
Reflection | Resolution: 1.3→34.025 Å / Num. all: 20526 / Num. obs: 20526 / % possible obs: 98.5 % / Observed criterion σ(F): 3 / Observed criterion σ(I): 3 / Redundancy: 10.25 % / Biso Wilson estimate: 15.079 Å2 / Rmerge(I) obs: 0.05 / Χ2: 0.98 / Net I/σ(I): 18.5 / Scaling rejects: 1592 |
Reflection shell | Resolution: 1.3→1.35 Å / Redundancy: 10 % / Rmerge(I) obs: 0.336 / Mean I/σ(I) obs: 5.4 / Num. measured all: 19857 / Num. unique all: 1978 / Χ2: 1.33 / % possible all: 96.5 |
-Phasing
Phasing | Method: molecular replacement | |||||||||
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Phasing MR | Model details: Phaser MODE: MR_AUTO
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.3→34.01 Å / Occupancy max: 1 / Occupancy min: 0.29 / SU ML: 0.21 / σ(F): 0.97 / 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 / Bsol: 49.747 Å2 / ksol: 0.447 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 36.16 Å2 / Biso mean: 16.266 Å2 / Biso min: 9.08 Å2
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Refinement step | Cycle: LAST / Resolution: 1.3→34.01 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 14
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