+Open data
-Basic information
Entry | Database: PDB / ID: 3a7f | ||||||
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Title | Human MST3 kinase | ||||||
Components | Serine/threonine kinase 24 (STE20 homolog, yeast) | ||||||
Keywords | TRANSFERASE / two-lobe protein kinase fold / ATP-binding / Kinase / Nucleotide-binding | ||||||
Function / homology | Function and homology information Apoptotic execution phase / regulation of axon regeneration / execution phase of apoptosis / intrinsic apoptotic signaling pathway in response to oxidative stress / positive regulation of axon regeneration / Apoptotic cleavage of cellular proteins / cellular response to starvation / negative regulation of cell migration / cellular response to oxidative stress / protein autophosphorylation ...Apoptotic execution phase / regulation of axon regeneration / execution phase of apoptosis / intrinsic apoptotic signaling pathway in response to oxidative stress / positive regulation of axon regeneration / Apoptotic cleavage of cellular proteins / cellular response to starvation / negative regulation of cell migration / cellular response to oxidative stress / protein autophosphorylation / non-specific serine/threonine protein kinase / protein kinase activity / intracellular signal transduction / cadherin binding / phosphorylation / Golgi membrane / protein phosphorylation / protein serine kinase activity / protein serine/threonine kinase activity / nucleolus / Golgi apparatus / signal transduction / extracellular exosome / nucleoplasm / ATP binding / nucleus / metal ion binding / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.55 Å | ||||||
Authors | Ko, T.P. / Jeng, W.Y. / Liu, C.I. / Lai, M.D. / Wang, A.H.J. | ||||||
Citation | Journal: Acta Crystallogr.,Sect.D / Year: 2010 Title: Structures of human MST3 kinase in complex with adenine, ADP and Mn2+. Authors: Ko, T.P. / Jeng, W.Y. / Liu, C.I. / Lai, M.D. / Wu, C.L. / Chang, W.J. / Shr, H.L. / Lu, T.J. / Wang, A.H.J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3a7f.cif.gz | 77.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3a7f.ent.gz | 57.4 KB | Display | PDB format |
PDBx/mmJSON format | 3a7f.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3a7f_validation.pdf.gz | 431.5 KB | Display | wwPDB validaton report |
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Full document | 3a7f_full_validation.pdf.gz | 438.2 KB | Display | |
Data in XML | 3a7f_validation.xml.gz | 16.9 KB | Display | |
Data in CIF | 3a7f_validation.cif.gz | 25 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/a7/3a7f ftp://data.pdbj.org/pub/pdb/validation_reports/a7/3a7f | HTTPS FTP |
-Related structure data
Related structure data | 3a7gC 3a7hC 3a7iC 3a7jC 2j7tS C: citing same article (ref.) 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 on special symmetry positions |
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-Components
#1: Protein | Mass: 34336.191 Da / Num. of mol.: 1 / Fragment: N-terminal kinase domain (UNP RESIDUES 1-303) Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: STK24 / Plasmid: pET-32 Xa/LIC / Production host: Escherichia coli (E. coli) / Strain (production host): ArcticExpress(DE3) / References: UniProt: Q6P0Y1, UniProt: Q9Y6E0*PLUS |
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#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.63 Å3/Da / Density % sol: 53.18 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: 50mM Tris-HCl, 100mM NaCl, 10%(v/v) glycerol, 5mM dithiothreitol, 0.1M Tris-HCl, 0.4M Na-formate, 10%(v/v) PEG 4000, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSRRC / Beamline: BL13B1 / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Sep 2, 2007 / Details: mirrors |
Radiation | Monochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.55→30 Å / Num. all: 51718 / Num. obs: 51285 / % possible obs: 99.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 1 / Redundancy: 5.5 % / Rmerge(I) obs: 0.03 / Net I/σ(I): 50.2 |
Reflection shell | Resolution: 1.55→1.61 Å / Redundancy: 5.4 % / Rmerge(I) obs: 0.527 / Mean I/σ(I) obs: 3 / Num. unique all: 5146 / % possible all: 99.7 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 2J7T Resolution: 1.55→30 Å / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.55→30 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.55→1.61 Å / Rfactor Rfree error: 0.0334
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