+Open data
-Basic information
Entry | Database: PDB / ID: 8s9w | |||||||||
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Title | Murine S100A7/S100A15 in presence of calcium | |||||||||
Components | Protein S100-A15A | |||||||||
Keywords | METAL BINDING PROTEIN / EF-Hand / Calcium binding protein / Nutritional immunity / Transition metal binding protein | |||||||||
Function / homology | Function and homology information zinc ion sequestering activity / RAGE receptor binding / : / chemoattractant activity / transition metal ion binding / calcium-dependent protein binding / inflammatory response / calcium ion binding / endoplasmic reticulum / extracellular space ...zinc ion sequestering activity / RAGE receptor binding / : / chemoattractant activity / transition metal ion binding / calcium-dependent protein binding / inflammatory response / calcium ion binding / endoplasmic reticulum / extracellular space / extracellular region / nucleus / cytosol / cytoplasm Similarity search - Function | |||||||||
Biological species | Mus musculus (house mouse) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.69 Å | |||||||||
Authors | Harrison, S.A. / Naretto, A. / Balakrishnan, S. / Chazin, W.J. | |||||||||
Funding support | United States, 2items
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Citation | Journal: J.Biol.Chem. / Year: 2023 Title: Comparative analysis of the physical properties of murine and human S100A7: Insight into why zinc piracy is mediated by human but not murine S100A7. Authors: Harrison, S.A. / Naretto, A. / Balakrishnan, S. / Perera, Y.R. / Chazin, W.J. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8s9w.cif.gz | 57.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8s9w.ent.gz | 40 KB | Display | PDB format |
PDBx/mmJSON format | 8s9w.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/s9/8s9w ftp://data.pdbj.org/pub/pdb/validation_reports/s9/8s9w | HTTPS FTP |
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-Related structure data
Similar structure data | Similarity search - Function & homologyF&H Search |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 11890.599 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Gene: S100a15a, S100a15, S100a7, S100a7a / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q6S5I3 |
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-Non-polymers , 6 types, 95 molecules
#2: Chemical | ChemComp-GOL / | ||||||||
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#3: Chemical | ChemComp-CA / #4: Chemical | ChemComp-SCN / #5: Chemical | #6: Chemical | ChemComp-ACT / | #7: Water | ChemComp-HOH / | |
-Details
Has ligand of interest | Y |
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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: 1.94 Å3/Da / Density % sol: 36.65 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop Details: 0.1 M of Potassium thiocyanate, 20% PEG MME 2K and 0.01M L-Proline |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.979 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Dec 11, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 1.69→34.16 Å / Num. obs: 21458 / % possible obs: 99.7 % / Redundancy: 13 % / CC1/2: 0.99 / Rmerge(I) obs: 0.07 / Net I/σ(I): 15.7 |
Reflection shell | Resolution: 1.69→1.73 Å / Mean I/σ(I) obs: 1.65 / Num. unique obs: 19412 / CC1/2: 0.81 / % possible all: 99.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.69→23.19 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.956 / SU B: 3.432 / SU ML: 0.104 / Cross valid method: THROUGHOUT / ESU R: 0.113 / ESU R Free: 0.117 / 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 mean: 38.697 Å2
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Refinement step | Cycle: 1 / Resolution: 1.69→23.19 Å
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