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Yorodumi- PDB-2c60: crystal structure of human mitogen-activated protein kinase kinas... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2c60 | ||||||
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Title | crystal structure of human mitogen-activated protein kinase kinase kinase 3 isoform 2 phox domain at 1.25 A resolution | ||||||
Components | HUMAN MITOGEN-ACTIVATED PROTEIN KINASE KINASE KINASE 3 ISOFORM 2 | ||||||
Keywords | TRANSFERASE / MAP3K3 / MAP/ERK KINASE KINASE 3 / MAPKKK3 / MEKK3 / SERINE THREONINE PHOSPHORYLATION / ATP-BINDING / KINASE / MAGNESIUM / METAL-BINDING / NUCLEOTIDE-BINDING / PHOSPHORYLATION / SERINE/THREONINE-PROTEIN KINASE | ||||||
Function / homology | Function and homology information positive regulation of cell proliferation in bone marrow / mitogen-activated protein kinase kinase kinase / positive regulation of p38MAPK cascade / positive regulation of cell migration involved in sprouting angiogenesis / blood vessel development / negative regulation of cellular senescence / MAP kinase kinase kinase activity / Interleukin-1 signaling / MAPK cascade / positive regulation of canonical NF-kappaB signal transduction ...positive regulation of cell proliferation in bone marrow / mitogen-activated protein kinase kinase kinase / positive regulation of p38MAPK cascade / positive regulation of cell migration involved in sprouting angiogenesis / blood vessel development / negative regulation of cellular senescence / MAP kinase kinase kinase activity / Interleukin-1 signaling / MAPK cascade / positive regulation of canonical NF-kappaB signal transduction / protein autophosphorylation / protein kinase activity / intracellular signal transduction / protein serine kinase activity / protein serine/threonine kinase activity / ATP binding / metal ion binding / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | HOMO SAPIENS (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.25 Å | ||||||
Authors | Debreczeni, J.E. / Salah, E. / Papagrigoriou, E. / Burgess, N. / von Delft, F. / Gileadi, O. / Sundstrom, M. / Edwards, A. / Arrowsmith, C. / Weigelt, J. / Knapp, S. | ||||||
Citation | Journal: To be Published Title: Crystal Structure of Human Mitogen-Activated Protein Kinase Kinase Kinase 3 Isoform 2 Fox Domain at 1.25 A Resolution Authors: Debreczeni, J.E. / Salah, E. / Papagrigoriou, E. / Burgess, N. / von Delft, F. / Gileadi, O. / Sundstrom, M. / Edwards, A. / Arrowsmith, C. / Weigelt, J. / Knapp, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2c60.cif.gz | 51.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2c60.ent.gz | 40.3 KB | Display | PDB format |
PDBx/mmJSON format | 2c60.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/c6/2c60 ftp://data.pdbj.org/pub/pdb/validation_reports/c6/2c60 | 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: 13144.145 Da / Num. of mol.: 1 / Fragment: PHOX DOMAIN, RESIDUES 37-124 Source method: isolated from a genetically manipulated source Source: (gene. exp.) HOMO SAPIENS (human) / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): R3 / References: UniProt: Q99759, EC: 2.7.1.37 | ||
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#2: Chemical | ChemComp-CA / | ||
#3: Chemical | ChemComp-GOL / | ||
#4: Water | ChemComp-HOH / | ||
Compound details | COMPONENT OF A PROTEIN KINASE SIGNAL TRANSDUCTISequence details | THE FIRST 13 RESIDUES (MHHHHHHSSG | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.1 Å3/Da / Density % sol: 42.1 % |
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Crystal grow | Method: vapor diffusion, sitting drop Details: 150 NANOLITRE SITTING DROPS, 0.2 KSCN, 20% PEG3350, 10% ETHYLENE GLYCOL |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.9718 |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Oct 22, 2005 / Details: MIRRORS |
Radiation | Monochromator: SI111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9718 Å / Relative weight: 1 |
Reflection | Resolution: 1.25→29.32 Å / Num. obs: 26421 / % possible obs: 93.8 % / Observed criterion σ(I): 3 / Redundancy: 5.78 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 15.81 |
Reflection shell | Resolution: 1.25→1.35 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.26 / Mean I/σ(I) obs: 5.25 / % possible all: 88.1 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 1.25→39.72 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.967 / SU B: 1.719 / SU ML: 0.032 / Cross valid method: THROUGHOUT / ESU R: 0.047 / ESU R Free: 0.043 / 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: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 15.02 Å2
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Refinement step | Cycle: LAST / Resolution: 1.25→39.72 Å
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