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Yorodumi- PDB-3ulr: Lysozyme contamination facilitates crystallization of a hetero-tr... -
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-Basic information
Entry | Database: PDB / ID: 3ulr | ||||||
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Title | Lysozyme contamination facilitates crystallization of a hetero-trimericCortactin:Arg:Lysozyme complex | ||||||
Components |
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Keywords | HYDROLASE / PROTEIN BINDING / SH3 / Protein-protein interaction | ||||||
Function / homology | Function and homology information lamellipodium organization / site of polarized growth / Arp2/3 complex binding / modification of postsynaptic actin cytoskeleton / modification of postsynaptic structure / mitotic spindle midzone / regulation of cell projection assembly / positive regulation of oxidoreductase activity / Role of ABL in ROBO-SLIT signaling / regulation of mitophagy ...lamellipodium organization / site of polarized growth / Arp2/3 complex binding / modification of postsynaptic actin cytoskeleton / modification of postsynaptic structure / mitotic spindle midzone / regulation of cell projection assembly / positive regulation of oxidoreductase activity / Role of ABL in ROBO-SLIT signaling / regulation of mitophagy / postsynaptic actin cytoskeleton / profilin binding / positive regulation of smooth muscle contraction / regulation of actin filament polymerization / positive regulation of chemotaxis / substrate-dependent cell migration, cell extension / focal adhesion assembly / regulation of cell motility / podosome / proline-rich region binding / exploration behavior / dendritic spine maintenance / negative regulation of Rho protein signal transduction / regulation of axon extension / cortical actin cytoskeleton / cortical cytoskeleton / positive regulation of actin filament polymerization / regulation of endocytosis / actin monomer binding / RAC3 GTPase cycle / positive regulation of T cell migration / regulation of cell adhesion / : / cellular response to retinoic acid / extrinsic apoptotic signaling pathway / clathrin-coated pit / voltage-gated potassium channel complex / ruffle / Negative regulation of FLT3 / positive regulation of establishment of T cell polarity / RAC1 GTPase cycle / phosphotyrosine residue binding / neuron projection morphogenesis / receptor-mediated endocytosis / Lactose synthesis / Antimicrobial peptides / regulation of autophagy / Neutrophil degranulation / negative regulation of extrinsic apoptotic signaling pathway / cell motility / actin filament / beta-N-acetylglucosaminidase activity / regulation of actin cytoskeleton organization / non-specific protein-tyrosine kinase / intracellular protein transport / non-membrane spanning protein tyrosine kinase activity / protein modification process / epidermal growth factor receptor signaling pathway / positive regulation of neuron projection development / peptidyl-tyrosine phosphorylation / actin filament binding / cell wall macromolecule catabolic process / actin cytoskeleton / lysozyme / cell junction / lamellipodium / lysozyme activity / manganese ion binding / cell cortex / positive regulation of cytosolic calcium ion concentration / actin cytoskeleton organization / postsynapse / regulation of apoptotic process / protein tyrosine kinase activity / defense response to Gram-negative bacterium / killing of cells of another organism / dendritic spine / cell adhesion / protein kinase activity / defense response to Gram-positive bacterium / defense response to bacterium / focal adhesion / glutamatergic synapse / Golgi apparatus / magnesium ion binding / endoplasmic reticulum / signal transduction / extracellular space / ATP binding / identical protein binding / plasma membrane / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | Gallus gallus (chicken) Mus musculus (house mouse) Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.65 Å | ||||||
Authors | Liu, W. / MacGrath, S. / Koleske, A.J. / Boggon, T.J. | ||||||
Citation | Journal: Acta Crystallogr.,Sect.F / Year: 2012 Title: Lysozyme contamination facilitates crystallization of a heterotrimeric cortactin-Arg-lysozyme complex. Authors: Liu, W. / Macgrath, S.M. / Koleske, A.J. / Boggon, T.J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3ulr.cif.gz | 60.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3ulr.ent.gz | 43.2 KB | Display | PDB format |
PDBx/mmJSON format | 3ulr.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3ulr_validation.pdf.gz | 441.3 KB | Display | wwPDB validaton report |
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Full document | 3ulr_full_validation.pdf.gz | 442.2 KB | Display | |
Data in XML | 3ulr_validation.xml.gz | 13.2 KB | Display | |
Data in CIF | 3ulr_validation.cif.gz | 19.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ul/3ulr ftp://data.pdbj.org/pub/pdb/validation_reports/ul/3ulr | HTTPS FTP |
-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: 14331.160 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: American Bioanalytical AB01178 / Source: (gene. exp.) Gallus gallus (chicken) / Gene: LYZ / References: UniProt: P00698, lysozyme |
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#2: Protein | Mass: 7202.915 Da / Num. of mol.: 1 / Fragment: SH3 domain (UNP residues 487-546) Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Gene: Cttn, Ems1 / Plasmid: pGEX6p-1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL 21 / References: UniProt: Q60598 |
#3: Protein/peptide | Mass: 1869.252 Da / Num. of mol.: 1 / Fragment: PXXP1 (UNP residues 563-579) / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P42684 |
#4: 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: 2.28 Å3/Da / Density % sol: 46.08 % |
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Crystal grow | Temperature: 297 K / Method: vapor diffusion, hanging drop / pH: 6 Details: 1.0M Na Citrate, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 297K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X6A / Wavelength: 1.0781 Å |
Detector | Type: ADSC QUANTUM 270 / Detector: CCD / Date: Oct 5, 2010 Details: Si(111) channel cut monochromator Toroidal focusing mirror |
Radiation | Monochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.0781 Å / Relative weight: 1 |
Reflection | Resolution: 1.65→20 Å / Num. all: 25122 / Num. obs: 23866 / % possible obs: 95 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.7 % / Biso Wilson estimate: 20.7 Å2 / Rsym value: 0.087 / Net I/σ(I): 14.9 |
Reflection shell | Resolution: 1.65→1.71 Å / Redundancy: 2.9 % / Mean I/σ(I) obs: 2.5 / Num. unique all: 1704 / Rsym value: 0.35 / % possible all: 65.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2D1X and 3M3U Resolution: 1.65→20 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.945 / SU B: 2.478 / SU ML: 0.083 / Cross valid method: THROUGHOUT / ESU R Free: 0.11 / Stereochemistry target values: Engh & Huber
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 24.167 Å2
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Refinement step | Cycle: LAST / Resolution: 1.65→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.651→1.694 Å / Total num. of bins used: 20
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