+Open data
-Basic information
Entry | Database: PDB / ID: 4pe1 | ||||||||||||
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Title | Crystal Structure of Calcium-loaded S100B bound to SC124 | ||||||||||||
Components | Protein S100-B | ||||||||||||
Keywords | METAL BINDING PROTEIN/INHIBITOR / malignant melanoma / calcium binding / complex / covalent inhibitor / METAL BINDING PROTEIN-INHIBITOR complex | ||||||||||||
Function / homology | Function and homology information 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 | Bos taurus (cattle) | ||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.576 Å | ||||||||||||
Authors | Cavalier, M.C. / Pierce, A.D. / Wilder, P.T. / Neau, D. / Toth, E.A. / Weber, D.J. | ||||||||||||
Funding support | United States, 3items
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Citation | Journal: Biochemistry / Year: 2014 Title: Covalent Small Molecule Inhibitors of Ca(2+)-Bound S100B. Authors: Cavalier, M.C. / Pierce, A.D. / Wilder, P.T. / Alasady, M.J. / Hartman, K.G. / Neau, D.B. / Foley, T.L. / Jadhav, A. / Maloney, D.J. / Simeonov, A. / Toth, E.A. / Weber, D.J. | ||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4pe1.cif.gz | 56.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4pe1.ent.gz | 38.9 KB | Display | PDB format |
PDBx/mmJSON format | 4pe1.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4pe1_validation.pdf.gz | 450.5 KB | Display | wwPDB validaton report |
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Full document | 4pe1_full_validation.pdf.gz | 451.8 KB | Display | |
Data in XML | 4pe1_validation.xml.gz | 11.6 KB | Display | |
Data in CIF | 4pe1_validation.cif.gz | 15.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/pe/4pe1 ftp://data.pdbj.org/pub/pdb/validation_reports/pe/4pe1 | HTTPS FTP |
-Related structure data
Related structure data | 4pdzC 4pe0C 4pe4C 4pe7C 1mhoS 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
#1: Protein | Mass: 10681.974 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bos taurus (cattle) / Gene: S100B / Production host: Escherichia coli (E. coli) / References: UniProt: P02638 #2: Chemical | #3: Chemical | ChemComp-CA / #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: 2.13 Å3/Da / Density % sol: 42.22 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, sitting drop / pH: 7 Details: 40% 2-methyl-2,4-pentanediol, 0.1M Hepes,7.5mM CaCl2, 4mM SC124 |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 1.1271 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 25, 2013 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1.1271 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.576→35.347 Å / Num. all: 23617 / Num. obs: 23617 / % possible obs: 97.8 % / Redundancy: 3.5 % / Rpim(I) all: 0.018 / Rrim(I) all: 0.034 / Rsym value: 0.029 / Net I/av σ(I): 11.77 / Net I/σ(I): 22.6 / Num. measured all: 83472 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1 / Rejects: _
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1MHO Resolution: 1.576→35.347 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 31.22 / 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: 70.1 Å2 / Biso mean: 28.9213 Å2 / Biso min: 13.27 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.576→35.347 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: 9
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