+Open data
-Basic information
Entry | Database: PDB / ID: 1k9p | ||||||
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Title | CRYSTAL STRUCTURE OF CALCIUM FREE (OR APO) HUMAN S100A6 | ||||||
Components | S100A6 | ||||||
Keywords | SIGNALING PROTEIN / S100A6 / CALCYCLIN / CALCIUM REGULATORY PROTEIN / CALCIUM FREE / APO / CACY | ||||||
Function / homology | Function and homology information 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 / extracellular exosome / zinc ion binding / extracellular region / nucleus / plasma membrane / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.9 Å | ||||||
Authors | Otterbein, L.R. / Dominguez, R. | ||||||
Citation | Journal: Structure / Year: 2002 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1k9p.cif.gz | 31.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1k9p.ent.gz | 20.6 KB | Display | PDB format |
PDBx/mmJSON format | 1k9p.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/k9/1k9p ftp://data.pdbj.org/pub/pdb/validation_reports/k9/1k9p | HTTPS FTP |
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-Related structure data
Related structure data | 1k8uSC 1k96C 1k9kC 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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Details | The second part of the biological assembly is generated by the two fold axis: x, -y, -z+1 |
-Components
#1: Protein | Mass: 10193.729 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: S100A6 / Plasmid: pAED4 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) pLYS / References: UniProt: P06703 |
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#2: Chemical | ChemComp-BME / |
#3: 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: 1.86 Å3/Da / Density % sol: 33.8 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 28% PEG 1500, 30 mM SODIUM CACODYLATE, 6% GLYCEROL,EGTA 2MM, pH 7.0, 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: ROTATING ANODE / Type: RIGAKU RUH3R / Wavelength: 1.54189 / Wavelength: 1 Å | |||||||||
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Nov 4, 1998 / Details: CHARLES SUPPER DOUBLE MIRROR X-RAY FOCUSING SYSTEM | |||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||
Radiation wavelength |
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Reflection | Resolution: 1.9→30 Å / Num. all: 6148 / Num. obs: 6136 / % possible obs: 99.8 % / Redundancy: 6.6 % / Biso Wilson estimate: 18.5 Å2 / Rmerge(I) obs: 0.069 / Net I/σ(I): 13.3 | |||||||||
Reflection shell | Resolution: 1.9→2 Å / Redundancy: 6 % / Rmerge(I) obs: 0.087 / Num. unique all: 1509 / % possible all: 99.7 | |||||||||
Reflection | *PLUS Highest resolution: 1.9 Å / Lowest resolution: 30 Å / Num. measured all: 40635 / Rmerge(I) obs: 0.069 | |||||||||
Reflection shell | *PLUS Rmerge(I) obs: 0.087 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: CALCIUM FREE S100A6 CYS3MET MUTANT (SELENOMETHIONINE DERIVATIVE)(PDB # 1K8U) Resolution: 1.9→30 Å / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0
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Refine analyze | Luzzati sigma a obs: 0.21 Å | |||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.9→30 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.9→1.97 Å / Rfactor Rfree error: 0.042
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Refinement | *PLUS Highest resolution: 1.9 Å / % reflection Rfree: 5 % / Rfactor obs: 0.176 / Rfactor Rfree: 0.182 / Rfactor Rwork: 0.176 | |||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||
LS refinement shell | *PLUS Rfactor Rfree: 0.216 / Rfactor Rwork: 0.199 |