+Open data
-Basic information
Entry | Database: PDB / ID: 1jnp | ||||||
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Title | Crystal Structure of Murine Tcl1 at 2.5 Resolution | ||||||
Components | T-CELL LEUKEMIA/LYMPHOMA PROTEIN 1A | ||||||
Keywords | IMMUNE SYSTEM / BETA BARREL / DIMER | ||||||
Function / homology | Function and homology information regulation of stem cell population maintenance / pronucleus / positive regulation of mitochondrial membrane potential / stem cell population maintenance / activation of protein kinase B activity / protein serine/threonine kinase activator activity / positive regulation of protein-containing complex assembly / positive regulation of protein serine/threonine kinase activity / positive regulation of peptidyl-serine phosphorylation / cellular response to tumor necrosis factor ...regulation of stem cell population maintenance / pronucleus / positive regulation of mitochondrial membrane potential / stem cell population maintenance / activation of protein kinase B activity / protein serine/threonine kinase activator activity / positive regulation of protein-containing complex assembly / positive regulation of protein serine/threonine kinase activity / positive regulation of peptidyl-serine phosphorylation / cellular response to tumor necrosis factor / cell cortex / negative regulation of gene expression / positive regulation of cell population proliferation / negative regulation of apoptotic process / protein kinase binding / endoplasmic reticulum / protein-containing complex / nucleoplasm / identical protein binding / nucleus / cytosol Similarity search - Function | ||||||
Biological species | Mus musculus (house mouse) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å | ||||||
Authors | Petock, J.M. / Torshin, I.Y. / Wang, Y.F. / DuBois, G.C. / Croce, C.M. / Harrison, R.W. / Weber, I.T. | ||||||
Citation | Journal: Acta Crystallogr.,Sect.D / Year: 2001 Title: Structure of murine Tcl1 at 2.5 A resolution and implications for the TCL oncogene family. Authors: Petock, J.M. / Torshin, I.Y. / Wang, Y.F. / Du Bois, G.C. / Croce, C.M. / Harrison, R.W. / Weber, I.T. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1jnp.cif.gz | 56.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1jnp.ent.gz | 41.1 KB | Display | PDB format |
PDBx/mmJSON format | 1jnp.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/jn/1jnp ftp://data.pdbj.org/pub/pdb/validation_reports/jn/1jnp | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 14098.037 Da / Num. of mol.: 2 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Production host: Escherichia coli (E. coli) / References: UniProt: P56280 #2: Water | ChemComp-HOH / | |
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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: 2.83 Å3/Da / Density % sol: 60.97 % | |||||||||||||||||||||||||
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 3.9 Details: Sodium Acetate, Tris, 1-O-octyl-beta-D-glucopyranoside, pH 3.9, VAPOR DIFFUSION, HANGING DROP, temperature 293K | |||||||||||||||||||||||||
Crystal grow | *PLUS pH: 7.5 / Method: vapor diffusion | |||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 90 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X12B / Wavelength: 1.037 |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Oct 11, 1999 |
Radiation | Monochromator: Double Flat Crystal Fixed-exit Monochromator, Si 111 Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.037 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→25 Å / Num. all: 11802 / Num. obs: 11802 / % possible obs: 97.5 % / Observed criterion σ(I): -3 / Rsym value: 0.058 / Net I/σ(I): 11.6 |
Reflection shell | Resolution: 2.5→2.54 Å / Rsym value: 0.264 / % possible all: 94.7 |
Reflection | *PLUS Lowest resolution: 10 Å / Num. obs: 11019 / % possible obs: 99.8 % / Num. measured all: 11802 / Rmerge(I) obs: 0.059 |
Reflection shell | *PLUS Lowest resolution: 2.59 Å / % possible obs: 99.5 % |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.5→10 Å / Num. parameters: 1813 / Num. restraintsaints: 2096 / Cross valid method: FREE R / Stereochemistry target values: ENGH AND HUBER
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Refine analyze | Num. disordered residues: 0 / Occupancy sum hydrogen: 0 / Occupancy sum non hydrogen: 1803 | |||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.5→10 Å
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Refine LS restraints |
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Software | *PLUS Name: SHELXL-97 / Classification: refinement | |||||||||||||||||||||||||||||||||
Refinement | *PLUS % reflection Rfree: 5 % / Rfactor all: 0.2257 / Rfactor Rwork: 0.196 | |||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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