+Open data
-Basic information
Entry | Database: PDB / ID: 7nrb | ||||||
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Title | Re-refinement of MK3-inhibitor complex | ||||||
Components | MAP kinase-activated protein kinase 3 | ||||||
Keywords | TRANSFERASE / kinase | ||||||
Function / homology | Function and homology information macropinocytosis / calcium-dependent protein serine/threonine kinase activity / mitogen-activated protein kinase binding / calcium/calmodulin-dependent protein kinase activity / toll-like receptor signaling pathway / MAP kinase kinase activity / vascular endothelial growth factor receptor signaling pathway / p38MAPK events / response to cytokine / activated TAK1 mediates p38 MAPK activation ...macropinocytosis / calcium-dependent protein serine/threonine kinase activity / mitogen-activated protein kinase binding / calcium/calmodulin-dependent protein kinase activity / toll-like receptor signaling pathway / MAP kinase kinase activity / vascular endothelial growth factor receptor signaling pathway / p38MAPK events / response to cytokine / activated TAK1 mediates p38 MAPK activation / VEGFA-VEGFR2 Pathway / peptidyl-serine phosphorylation / Oxidative Stress Induced Senescence / response to lipopolysaccharide / calmodulin binding / non-specific serine/threonine protein kinase / intracellular signal transduction / protein serine kinase activity / protein serine/threonine kinase activity / signal transduction / nucleoplasm / ATP binding / nucleus / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å | ||||||
Authors | Croll, T.I. / Read, R.J. | ||||||
Funding support | United Kingdom, 1items
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Citation | Journal: Acta Crystallogr D Struct Biol / Year: 2021 Title: Adaptive Cartesian and torsional restraints for interactive model rebuilding. Authors: Croll, T.I. / Read, R.J. #1: Journal: Acta Crystallogr D Struct Biol / Year: 2018 Title: ISOLDE: a physically realistic environment for model building into low-resolution electron-density maps. Authors: Croll, T.I. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7nrb.cif.gz | 90.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7nrb.ent.gz | 53.9 KB | Display | PDB format |
PDBx/mmJSON format | 7nrb.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7nrb_validation.pdf.gz | 754.1 KB | Display | wwPDB validaton report |
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Full document | 7nrb_full_validation.pdf.gz | 757.2 KB | Display | |
Data in XML | 7nrb_validation.xml.gz | 13.6 KB | Display | |
Data in CIF | 7nrb_validation.cif.gz | 18.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/nr/7nrb ftp://data.pdbj.org/pub/pdb/validation_reports/nr/7nrb | HTTPS FTP |
-Related structure data
Related structure data | 7nryC 3fhrS S: Starting model for refinement C: citing same article (ref.) |
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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
#1: Protein | Mass: 38574.980 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: MAPKAPK3 / Production host: Escherichia coli (E. coli) References: UniProt: Q16644, non-specific serine/threonine protein kinase |
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#2: Chemical | ChemComp-P4O / |
#3: Water | ChemComp-HOH / |
Has ligand of interest | N |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.38 Å3/Da / Density % sol: 48.28 % |
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Crystal grow | Temperature: 296 K / Method: vapor diffusion, sitting drop Details: 10%-15% PEG 3350, 100mM BisTris propane/citric acid, pH 5.0, VAPOR DIFFUSION, SITTING DROP, temperature 296K |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.9769 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 30, 2008 |
Radiation | Monochromator: double Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9769 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→31.43 Å / Num. obs: 27952 / % possible obs: 97.9 % / Redundancy: 3.37 % / Biso Wilson estimate: 38.25 Å2 / Rmerge(I) obs: 0.051 / Net I/σ(I): 10.3 |
Reflection shell | Resolution: 1.9→1.97 Å / Rmerge(I) obs: 0.451 / Num. unique obs: 2500 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3fhr Resolution: 1.9→27.78 Å / SU ML: 0.3909 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 33.7404 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 47.59 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.9→27.78 Å
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Refine LS restraints |
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LS refinement shell |
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