[English] 日本語
Yorodumi- PDB-1jks: 1.5A X-RAY STRUCTURE OF APO FORM OF A CATALYTIC DOMAIN OF DEATH-A... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1jks | ||||||
---|---|---|---|---|---|---|---|
Title | 1.5A X-RAY STRUCTURE OF APO FORM OF A CATALYTIC DOMAIN OF DEATH-ASSOCIATED PROTEIN KINASE | ||||||
Components | DEATH-ASSOCIATED PROTEIN KINASE | ||||||
Keywords | TRANSFERASE | ||||||
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 / regulation of NMDA receptor activity / syntaxin-1 binding / calcium/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 / regulation of NMDA receptor activity / syntaxin-1 binding / calcium/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 / non-specific serine/threonine protein kinase / calmodulin binding / 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 / SAD / Resolution: 1.5 Å | ||||||
Authors | Tereshko, V. / Teplova, M. / Brunzelle, J. / Watterson, D.M. / Egli, M. | ||||||
Citation | Journal: Nat.Struct.Biol. / Year: 2001 Title: Crystal structures of the catalytic domain of human protein kinase associated with apoptosis and tumor suppression. Authors: Tereshko, V. / Teplova, M. / Brunzelle, J. / Watterson, D.M. / Egli, M. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 1jks.cif.gz | 76.7 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb1jks.ent.gz | 56.9 KB | Display | PDB format |
PDBx/mmJSON format | 1jks.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1jks_validation.pdf.gz | 431.8 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 1jks_full_validation.pdf.gz | 439.4 KB | Display | |
Data in XML | 1jks_validation.xml.gz | 16.5 KB | Display | |
Data in CIF | 1jks_validation.cif.gz | 24.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/jk/1jks ftp://data.pdbj.org/pub/pdb/validation_reports/jk/1jks | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 33794.367 Da / Num. of mol.: 1 / Fragment: CATALYTIC DOMAIN, PROTEIN KINASE DOMAIN Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) References: UniProt: P53355, Transferases; Transferring phosphorus-containing groups; Phosphotransferases with an alcohol group as acceptor |
---|---|
#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 1.92 Å3/Da / Density % sol: 36.02 % | |||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Crystal grow | pH: 7.5 / Details: pH 7.50 | |||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS pH: 7.5 / Method: vapor diffusion, hanging drop | |||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
|
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 5ID-B / Wavelength: 1.0098 |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Sep 5, 2000 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.0098 Å / Relative weight: 1 |
Reflection | Resolution: 3→20 Å / Num. obs: 41549 / % possible obs: 97.7 % / Observed criterion σ(I): -3 / Redundancy: 5.4 % / Biso Wilson estimate: 17.7 Å2 / Rmerge(I) obs: 0.037 |
Reflection shell | Resolution: 1.5→1.55 Å / Rmerge(I) obs: 0.27 / % possible all: 94.2 |
Reflection | *PLUS Highest resolution: 1.5 Å / Lowest resolution: 20 Å / Rmerge(I) obs: 0.037 |
Reflection shell | *PLUS % possible obs: 94.2 % / Num. unique obs: 3938 / Rmerge(I) obs: 0.27 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: SAD / Resolution: 1.5→19.68 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 571669.06 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Solvent model: FLAT MODEL / Bsol: 56.9883 Å2 / ksol: 0.409931 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 21.1 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.5→19.68 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 1.5→1.59 Å / Rfactor Rfree error: 0.009 / Total num. of bins used: 6
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Rfactor obs: 0.183 / Rfactor Rfree: 0.202 / Rfactor Rwork: 0.183 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | *PLUS Rfactor Rfree: 0.236 / Rfactor Rwork: 0.209 |