+Open data
-Basic information
Entry | Database: PDB / ID: 3iqq | ||||||
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Title | X-ray structure of bovine TRTK12-Ca(2+)-S100B | ||||||
Components |
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Keywords | METAL BINDING PROTEIN / EF hand / Alpha helical / Metal-binding / Nucleus | ||||||
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 / axonogenesis / astrocyte activation / tau protein binding / calcium-dependent protein binding / regulation of translation / positive regulation of canonical NF-kappaB signal transduction / learning or memory / cell adhesion / phosphorylation / calcium ion binding / positive regulation of cell population proliferation / protein homodimerization activity / extracellular space / zinc ion binding / extracellular region / nucleus / cytoplasm Similarity search - Function | ||||||
Biological species | Bos taurus (cattle) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.01 Å | ||||||
Authors | Charpentier, T.H. / Weber, D.J. / Toth, E.A. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2010 Title: The Effects of CapZ Peptide (TRTK-12) Binding to S100B-Ca(2+) as Examined by NMR and X-ray Crystallography Authors: Charpentier, T.H. / Thompson, L.E. / Liriano, M.A. / Varney, K.M. / Wilder, P.T. / Pozharski, E. / 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 | 3iqq.cif.gz | 36.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3iqq.ent.gz | 23.8 KB | Display | PDB format |
PDBx/mmJSON format | 3iqq.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/iq/3iqq ftp://data.pdbj.org/pub/pdb/validation_reports/iq/3iqq | HTTPS FTP |
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-Related structure data
Related structure data | 3iqoC 1mhoS 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: 10681.974 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bos taurus (cattle) / Gene: S100B / Plasmid: pET11b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P02638 | ||
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#2: Protein/peptide | Mass: 1477.728 Da / Num. of mol.: 1 / Source method: obtained synthetically Details: The peptide was synthesized using solid-state peptide synthesis | ||
#3: Chemical | #4: 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: 1.9 Å3/Da / Density % sol: 31.28 % |
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Crystal grow | Temperature: 295 K / Method: sitting drop / pH: 6.8 Details: 26% PEG3350, 7.5mM CaCl2, 100mM Cacodylate buffer, pH 6.8, sitting drop, temperature 295K |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.5418 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Mar 31, 2006 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.01→35.69 Å / Num. obs: 6057 / % possible obs: 98.2 % / Redundancy: 12.7 % / Rmerge(I) obs: 0.066 / Χ2: 1.085 / Net I/σ(I): 15.6 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Phasing
Phasing | Method: molecular replacement | |||||||||
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Phasing MR | Model details: Phaser MODE: MR_AUTO
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 1MHO Resolution: 2.01→35.69 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.935 / WRfactor Rfree: 0.323 / WRfactor Rwork: 0.255 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.807 / SU B: 10.561 / SU ML: 0.153 / SU R Cruickshank DPI: 0.268 / SU Rfree: 0.214 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.264 / ESU R Free: 0.207 / 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: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 58.98 Å2 / Biso mean: 34.734 Å2 / Biso min: 27.14 Å2
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Refinement step | Cycle: LAST / Resolution: 2.01→35.69 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.009→2.061 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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