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- PDB-5hlv: Crystal structure of calcium and zinc-bound human S100A8 in space... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5hlv | ||||||
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Title | Crystal structure of calcium and zinc-bound human S100A8 in space group P212121 | ||||||
![]() | Protein S100-A8 | ||||||
![]() | SIGNALING PROTEIN / S100 proteins / calcium / zinc / oligomer | ||||||
Function / homology | ![]() sequestering of zinc ion / calprotectin complex / neutrophil aggregation / positive regulation of peptide secretion / autocrine signaling / Toll-like receptor 4 binding / chronic inflammatory response / Metal sequestration by antimicrobial proteins / RAGE receptor binding / leukocyte migration involved in inflammatory response ...sequestering of zinc ion / calprotectin complex / neutrophil aggregation / positive regulation of peptide secretion / autocrine signaling / Toll-like receptor 4 binding / chronic inflammatory response / Metal sequestration by antimicrobial proteins / RAGE receptor binding / leukocyte migration involved in inflammatory response / peptide secretion / Regulation of TLR by endogenous ligand / astrocyte development / MyD88 deficiency (TLR2/4) / intermediate filament cytoskeleton / arachidonate binding / IRAK4 deficiency (TLR2/4) / MyD88:MAL(TIRAP) cascade initiated on plasma membrane / response to zinc ion / regulation of toll-like receptor signaling pathway / regulation of cytoskeleton organization / peptidyl-cysteine S-nitrosylation / RHO GTPases Activate NADPH Oxidases / defense response to fungus / positive regulation of intrinsic apoptotic signaling pathway / neutrophil chemotaxis / autophagy / positive regulation of inflammatory response / activation of cysteine-type endopeptidase activity involved in apoptotic process / calcium-dependent protein binding / positive regulation of NF-kappaB transcription factor activity / ER-Phagosome pathway / positive regulation of cell growth / microtubule binding / secretory granule lumen / collagen-containing extracellular matrix / response to ethanol / response to lipopolysaccharide / cytoskeleton / defense response to bacterium / inflammatory response / innate immune response / calcium ion binding / Neutrophil degranulation / apoptotic process / extracellular space / extracellular exosome / zinc ion binding / extracellular region / nucleus / plasma membrane / cytosol Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Lin, H. / Andersen, G.R. / Yatime, L. | ||||||
![]() | ![]() Title: Crystal structure of human S100A8 in complex with zinc and calcium. Authors: Lin, H. / Andersen, G.R. / Yatime, L. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 311.5 KB | Display | ![]() |
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PDB format | ![]() | 254.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 5hloC ![]() 1mr8S 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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2 | ![]()
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3 | ![]()
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4 | ![]()
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Unit cell |
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Components
-Protein , 1 types, 8 molecules ABCDEFGH
#1: Protein | Mass: 10924.606 Da / Num. of mol.: 8 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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-Non-polymers , 5 types, 390 molecules ![](data/chem/img/CA.gif)
![](data/chem/img/ZN.gif)
![](data/chem/img/ACT.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/ZN.gif)
![](data/chem/img/ACT.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-CA / #3: Chemical | ChemComp-ZN / #4: Chemical | ChemComp-ACT / #5: Chemical | #6: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.47 Å3/Da / Density % sol: 50.3 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4 Details: 0.2 M ammonium acetate, 0.1 M Na acetate pH 4.0, 15% PEG 3350, 0.4% 2,2,2-trifluoroethanol |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jun 29, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→50 Å / Num. obs: 42972 / % possible obs: 96.5 % / Redundancy: 6.1 % / Rsym value: 0.148 / Net I/σ(I): 12.54 |
Reflection shell | Resolution: 2.2→2.3 Å / Redundancy: 6 % / Mean I/σ(I) obs: 3.08 / % possible all: 99.6 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1MR8 Resolution: 2.2→40.26 Å / SU ML: 0.23 / Cross valid method: FREE R-VALUE / σ(F): 2 / Phase error: 21.71 / 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 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.2→40.26 Å
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Refine LS restraints |
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LS refinement shell |
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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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