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Open data
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Basic information
Entry | Database: PDB / ID: 1k9k | ||||||
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Title | CRYSTAL STRUCTURE OF CALCIUM BOUND HUMAN S100A6 | ||||||
![]() | S100A6 | ||||||
![]() | SIGNALING PROTEIN / S100A6 / CALCYCLIN / CALCIUM REGULATORY PROTEIN / CALCIUM BOUND / CACY | ||||||
Function / homology | ![]() monoatomic ion transmembrane transporter activity / S100 protein binding / tropomyosin binding / ruffle / axonogenesis / cytoplasmic side of plasma membrane / calcium-dependent protein binding / positive regulation of fibroblast proliferation / nuclear envelope / collagen-containing extracellular matrix ...monoatomic ion transmembrane transporter activity / S100 protein binding / tropomyosin binding / ruffle / axonogenesis / cytoplasmic side of plasma membrane / calcium-dependent protein binding / positive regulation of fibroblast proliferation / nuclear envelope / collagen-containing extracellular matrix / calcium ion binding / perinuclear region of cytoplasm / signal transduction / protein homodimerization activity / zinc ion binding / extracellular exosome / extracellular region / nucleus / plasma membrane / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Otterbein, L.R. / Dominguez, R. | ||||||
![]() | ![]() Title: Crystal structures of S100A6 in the Ca(2+)-free and Ca(2+)-bound states: the calcium sensor mechanism of S100 proteins revealed at atomic resolution. Authors: Otterbein, L.R. / Kordowska, J. / Witte-Hoffmann, C. / Wang, C.L. / Dominguez, R. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 52.3 KB | Display | ![]() |
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PDB format | ![]() | 36.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 376.7 KB | Display | ![]() |
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Full document | ![]() | 378.3 KB | Display | |
Data in XML | ![]() | 5.2 KB | Display | |
Data in CIF | ![]() | 8.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1k8uC ![]() 1k96C ![]() 1k9pC ![]() 1psrS 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: 10193.729 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Chemical | ChemComp-CA / #3: Chemical | #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.1 Å3/Da / Density % sol: 42 % | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.8 Details: 20% PEG 5000 MME, 30 mM TRIS-HCL, 8% GLYCEROL, pH 7.8, VAPOR DIFFUSION, HANGING DROP, temperature 293K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 20 ℃ / pH: 6.5 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Dec 7, 2000 / Details: BENT CYLINDRICAL SI- MIRROR (RH COATING) |
Radiation | Monochromator: SI(III) DOUBLE CRYSTAL MONOCHROMATOR, L1=1 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.75→19.2 Å / Num. all: 17303 / Num. obs: 16853 / % possible obs: 97.4 % / Observed criterion σ(I): 0 / Redundancy: 4.4 % / Biso Wilson estimate: 19.27 Å2 / Rmerge(I) obs: 0.062 / Net I/σ(I): 9.9 |
Reflection shell | Resolution: 1.75→1.89 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.192 / Num. unique all: 3218 / % possible all: 96.6 |
Reflection | *PLUS Num. measured all: 74706 / Rmerge(I) obs: 0.062 |
Reflection shell | *PLUS Rmerge(I) obs: 0.192 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PSORIASIN S100A7 (PBD # 1PSR) Resolution: 1.76→19.2 Å / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0
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Refine analyze | Luzzati sigma a obs: 0.11 Å | |||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.76→19.2 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.76→1.9 Å / Rfactor Rfree error: 0.11
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Refinement | *PLUS % reflection Rfree: 5 % / Rfactor obs: 0.185 / Rfactor Rfree: 0.199 / Rfactor Rwork: 0.185 | |||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||
LS refinement shell | *PLUS Rfactor Rfree: 0.227 / Rfactor Rwork: 0.206 |