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Open data
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Basic information
Entry | Database: PDB / ID: 5dkr | ||||||||||||
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Title | Crystal Structure of Calcium-loaded S100B bound to SBi29 | ||||||||||||
![]() | Protein S100-B | ||||||||||||
![]() | METAL BINDING PROTEIN/INHIBITOR / malignant melanoma / calcium binding / complex / covalent inhibitor / METAL BINDING PROTEIN-INHIBITOR complex | ||||||||||||
Function / homology | ![]() Advanced glycosylation endproduct receptor signaling / TRAF6 mediated NF-kB activation / TAK1-dependent IKK and NF-kappa-B activation / adaptive thermogenesis / kinase inhibitor activity / sympathetic neuron projection extension / positive regulation of complement activation / RAGE receptor binding / negative regulation of monocyte chemotactic protein-1 production / S100 protein binding ...Advanced glycosylation endproduct receptor signaling / TRAF6 mediated NF-kB activation / TAK1-dependent IKK and NF-kappa-B activation / adaptive thermogenesis / kinase inhibitor activity / sympathetic neuron projection extension / positive regulation of complement activation / RAGE receptor binding / negative regulation of monocyte chemotactic protein-1 production / S100 protein binding / astrocyte activation / phosphorylation / axonogenesis / tau protein binding / calcium-dependent protein binding / regulation of translation / positive regulation of canonical NF-kappaB signal transduction / learning or memory / cell adhesion / positive regulation of cell population proliferation / calcium ion binding / protein homodimerization activity / extracellular space / zinc ion binding / extracellular region / nucleus / cytoplasm Similarity search - Function | ||||||||||||
Biological species | ![]() ![]() | ||||||||||||
Method | ![]() ![]() ![]() | ||||||||||||
![]() | Cavalier, M.C. / Ansari, M.I. / Pierce, A.D. / Wilder, P.T. / McKnight, L.E. / Raman, E.P. / Neau, D.B. / Bezawada, P. / Alasady, M.J. / Varney, K.M. ...Cavalier, M.C. / Ansari, M.I. / Pierce, A.D. / Wilder, P.T. / McKnight, L.E. / Raman, E.P. / Neau, D.B. / Bezawada, P. / Alasady, M.J. / Varney, K.M. / Toth, E.A. / MacKerell Jr., A.D. / Coop, A. / Weber, D.J. | ||||||||||||
Funding support | ![]()
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![]() | ![]() Title: Small Molecule Inhibitors of Ca(2+)-S100B Reveal Two Protein Conformations. Authors: Cavalier, M.C. / Ansari, M.I. / Pierce, A.D. / Wilder, P.T. / McKnight, L.E. / Raman, E.P. / Neau, D.B. / Bezawada, P. / Alasady, M.J. / Charpentier, T.H. / Varney, K.M. / Toth, E.A. / ...Authors: Cavalier, M.C. / Ansari, M.I. / Pierce, A.D. / Wilder, P.T. / McKnight, L.E. / Raman, E.P. / Neau, D.B. / Bezawada, P. / Alasady, M.J. / Charpentier, T.H. / Varney, K.M. / Toth, E.A. / MacKerell, A.D. / Coop, A. / Weber, D.J. | ||||||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 58.5 KB | Display | ![]() |
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PDB format | ![]() | 40 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 665.2 KB | Display | ![]() |
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Full document | ![]() | 665.5 KB | Display | |
Data in XML | ![]() | 11.1 KB | Display | |
Data in CIF | ![]() | 15.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5dknC ![]() 5dkqC ![]() 1mhoS C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 10681.974 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #2: Chemical | ChemComp-CA / #3: Chemical | ChemComp-5CZ / | #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.34 Å3/Da / Density % sol: 47.54 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, sitting drop Details: 40% 2-methyl-2,4-pentanediol; 0.1M Hepes, pH 7.0, 7.5mM CaCl2 Temp details: 7 |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | |||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 14, 2013 | |||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1.127092 Å / Relative weight: 1 | |||||||||||||||||||||||||||
Reflection | Resolution: 1.74→33.3 Å / Num. obs: 20972 / % possible obs: 98.7 % / Redundancy: 3.9 % / Biso Wilson estimate: 28.49 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.059 / Rpim(I) all: 0.033 / Net I/σ(I): 11.8 / Num. measured all: 82661 | |||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1 / Rejects: _
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1MHO Resolution: 1.742→33.298 Å / FOM work R set: 0.7799 / SU ML: 0.24 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 28.12 / Stereochemistry target values: ML
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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 max: 63.04 Å2 / Biso mean: 30.22 Å2 / Biso min: 14.5 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.742→33.298 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 14
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