+Open data
-Basic information
Entry | Database: PDB / ID: 1cm8 | ||||||
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Title | PHOSPHORYLATED MAP KINASE P38-GAMMA | ||||||
Components | PHOSPHORYLATED MAP KINASE P38-GAMMA | ||||||
Keywords | TRANSFERASE / P38-GAMMA / GAMMA / PHOSPHORYLATION / MAP KINASE | ||||||
Function / homology | Function and homology information positive regulation of peptidase activity / myoblast differentiation / Activation of PPARGC1A (PGC-1alpha) by phosphorylation / muscle organ development / positive regulation of muscle cell differentiation / Myogenesis / negative regulation of cell cycle / MAP kinase activity / mitogen-activated protein kinase / signal transduction in response to DNA damage ...positive regulation of peptidase activity / myoblast differentiation / Activation of PPARGC1A (PGC-1alpha) by phosphorylation / muscle organ development / positive regulation of muscle cell differentiation / Myogenesis / negative regulation of cell cycle / MAP kinase activity / mitogen-activated protein kinase / signal transduction in response to DNA damage / p38MAPK events / NOD1/2 Signaling Pathway / VEGFA-VEGFR2 Pathway / Negative regulation of MAPK pathway / MAPK cascade / peptidyl-serine phosphorylation / regulation of cell cycle / intracellular signal transduction / protein serine kinase activity / protein serine/threonine kinase activity / magnesium ion binding / signal transduction / mitochondrion / nucleoplasm / ATP binding / nucleus / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 2.4 Å | ||||||
Authors | Bellon, S. / Fitzgibbon, M.J. / Fox, T. / Hsiao, H.M. / Wilson, K.P. | ||||||
Citation | Journal: Structure Fold.Des. / Year: 1999 Title: The structure of phosphorylated p38gamma is monomeric and reveals a conserved activation-loop conformation. Authors: Bellon, S. / Fitzgibbon, M.J. / Fox, T. / Hsiao, H.M. / Wilson, K.P. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1cm8.cif.gz | 150.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1cm8.ent.gz | 115.8 KB | Display | PDB format |
PDBx/mmJSON format | 1cm8.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1cm8_validation.pdf.gz | 533.4 KB | Display | wwPDB validaton report |
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Full document | 1cm8_full_validation.pdf.gz | 554.4 KB | Display | |
Data in XML | 1cm8_validation.xml.gz | 18.7 KB | Display | |
Data in CIF | 1cm8_validation.cif.gz | 26.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/cm/1cm8 ftp://data.pdbj.org/pub/pdb/validation_reports/cm/1cm8 | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS oper: (Code: given Matrix: (-0.0105, -0.9989, -0.0454), Vector: |
-Components
#1: Protein | Mass: 42157.090 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / References: UniProt: P53778 #2: Chemical | ChemComp-MG / #3: Chemical | #4: 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: 2.59 Å3/Da / Density % sol: 52.52 % | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Method: vapor diffusion / pH: 7 / Details: pH 7.0, VAPOR DIFFUSION | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS pH: 8.5 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 110 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 1.1 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.1 Å / Relative weight: 1 |
Reflection | Resolution: 2.4→50 Å / Num. obs: 31732 / % possible obs: 89.9 % / Redundancy: 3.7 % / Rsym value: 6.7 / Net I/σ(I): 9.8 |
Reflection | *PLUS Num. measured all: 118429 / Rmerge(I) obs: 0.067 |
Reflection shell | *PLUS Highest resolution: 2.4 Å / Lowest resolution: 2.49 Å / % possible obs: 76.5 % |
-Processing
Software |
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Refinement | Method to determine structure: MIR / Resolution: 2.4→50 Å / Rfactor Rfree error: 0.006 / Cross valid method: THROUGHOUT / σ(F): 2 Details: THE DATA ARE EXTREMELY ANISOTROPIC. THIS RESULTED IN LESS THAN 100% COMPLETENESS FOR THE NATIVE DATA.
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Refinement step | Cycle: LAST / Resolution: 2.4→50 Å
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Refine LS restraints |
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Refine LS restraints NCS | NCS model details: RESTRAINTS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Software | *PLUS Name: CNS / Version: 0.2 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Highest resolution: 2.4 Å / Lowest resolution: 50 Å / σ(F): 2 / % reflection Rfree: 9.9 % / Rfactor obs: 0.232 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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