+Open data
-Basic information
Entry | Database: PDB / ID: 2y0a | ||||||
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Title | Structure of DAPK1 construct residues 1-304 | ||||||
Components | DEATH-ASSOCIATED PROTEIN KINASE 1DAPK1 | ||||||
Keywords | TRANSFERASE / CALMODULIN / ESPRIT | ||||||
Function / homology | Function and homology information cellular response to hydroperoxide / regulation of response to tumor cell / positive regulation of autophagic cell death / DAPK1-calmodulin complex / defense response to tumor cell / Caspase activation via Dependence Receptors in the absence of ligand / syntaxin-1 binding / regulation of NMDA receptor activity / calmodulin-dependent protein kinase activity / positive regulation of cysteine-type endopeptidase activity involved in apoptotic process ...cellular response to hydroperoxide / regulation of response to tumor cell / positive regulation of autophagic cell death / DAPK1-calmodulin complex / defense response to tumor cell / Caspase activation via Dependence Receptors in the absence of ligand / syntaxin-1 binding / regulation of NMDA receptor activity / calmodulin-dependent protein kinase activity / positive regulation of cysteine-type endopeptidase activity involved in apoptotic process / extrinsic apoptotic signaling pathway via death domain receptors / positive regulation of autophagy / regulation of autophagy / apoptotic signaling pathway / cellular response to type II interferon / actin cytoskeleton / regulation of apoptotic process / protein autophosphorylation / postsynaptic density / negative regulation of translation / calmodulin binding / non-specific serine/threonine protein kinase / protein kinase activity / intracellular signal transduction / positive regulation of apoptotic process / protein phosphorylation / protein serine kinase activity / protein serine/threonine kinase activity / glutamatergic synapse / apoptotic process / GTP binding / negative regulation of apoptotic process / ATP binding / identical protein binding / nucleus / plasma membrane / cytoplasm Similarity search - Function | ||||||
Biological species | HOMO SAPIENS (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å | ||||||
Authors | Yumerefendi, H. / Mas, P.J. / Dordevic, N. / McCarthy, A.A. / Hart, D.J. | ||||||
Citation | Journal: To be Published Title: Library-Based Construct Screening of Death-Associated Protein Kinase 1 Identifies the Minimal Calmodulin Interaction Region and Autoinhibitory Conformation of the Catalytic Domain Authors: Yumerefendi, H. / Mas, P.J. / Dordevic, N. / Mccarthy, A.A. / Hart, D.J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2y0a.cif.gz | 73.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2y0a.ent.gz | 54 KB | Display | PDB format |
PDBx/mmJSON format | 2y0a.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/y0/2y0a ftp://data.pdbj.org/pub/pdb/validation_reports/y0/2y0a | HTTPS FTP |
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-Related structure data
Related structure data | 1ig1S 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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Unit cell |
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-Components
#1: Protein | Mass: 37266.348 Da / Num. of mol.: 1 / Fragment: KINASE CATALYTIC DOMAIN, RESIDUES 2-304 Source method: isolated from a genetically manipulated source Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PYUM6002/PET-9A / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) References: UniProt: P53355, non-specific serine/threonine protein kinase |
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#2: Chemical | ChemComp-MES / |
#3: Water | ChemComp-HOH / |
Sequence details | LAST 22 AMINO ACIDS FROM A BIOTIN ACCEPTOR TAG |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.97 Å3/Da / Density % sol: 58.6 % |
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Crystal grow | pH: 6 / Details: 5% PEG 6000, 0.1M MES, PH 6.0 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.8726 |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Sep 15, 2009 / Details: KB MIRROR SYSTEM |
Radiation | Monochromator: SI111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.8726 Å / Relative weight: 1 |
Reflection | Resolution: 2.6→50 Å / Num. obs: 14084 / % possible obs: 92.9 % / Observed criterion σ(I): 0 / Redundancy: 4 % / Biso Wilson estimate: 40.8 Å2 / Rmerge(I) obs: 0.1 / Net I/σ(I): 12.3 |
Reflection shell | Resolution: 2.6→2.7 Å / Redundancy: 4 % / Rmerge(I) obs: 0.65 / Mean I/σ(I) obs: 2.3 / % possible all: 79.8 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1IG1 Resolution: 2.6→50 Å / Cor.coef. Fo:Fc: 0.941 / Cor.coef. Fo:Fc free: 0.912 / SU B: 9.999 / SU ML: 0.214 / Cross valid method: THROUGHOUT / ESU R: 0.44 / ESU R Free: 0.294 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
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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 mean: 40.968 Å2
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Refinement step | Cycle: LAST / Resolution: 2.6→50 Å
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