+Open data
-Basic information
Entry | Database: PDB / ID: 1s18 | ||||||
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Title | Structure and protein design of human apyrase | ||||||
Components | apyrase | ||||||
Keywords | HYDROLASE / ADPase / five-blade beta propeller / calcium-binding protein / nucleotide-binding motif | ||||||
Function / homology | Function and homology information nucleoside diphosphate phosphatase / UDP phosphatase activity / ADP phosphatase activity / GDP phosphatase activity / proteoglycan biosynthetic process / Golgi cisterna membrane / specific granule lumen / tertiary granule lumen / positive regulation of canonical NF-kappaB signal transduction / ficolin-1-rich granule lumen ...nucleoside diphosphate phosphatase / UDP phosphatase activity / ADP phosphatase activity / GDP phosphatase activity / proteoglycan biosynthetic process / Golgi cisterna membrane / specific granule lumen / tertiary granule lumen / positive regulation of canonical NF-kappaB signal transduction / ficolin-1-rich granule lumen / calcium ion binding / Neutrophil degranulation / endoplasmic reticulum membrane / Golgi apparatus / protein homodimerization activity / extracellular exosome / extracellular region / membrane / plasma membrane Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.7 Å | ||||||
Authors | Dai, J. / Liu, J. / Deng, Y. / Smith, T.M. / Lu, M. | ||||||
Citation | Journal: Cell(Cambridge,Mass.) / Year: 2004 Title: Structure and protein design of a human platelet function inhibitor. Authors: Dai, J. / Liu, J. / Deng, Y. / Smith, T.M. / Lu, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1s18.cif.gz | 150.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1s18.ent.gz | 117.3 KB | Display | PDB format |
PDBx/mmJSON format | 1s18.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1s18_validation.pdf.gz | 462.9 KB | Display | wwPDB validaton report |
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Full document | 1s18_full_validation.pdf.gz | 470.3 KB | Display | |
Data in XML | 1s18_validation.xml.gz | 30.5 KB | Display | |
Data in CIF | 1s18_validation.cif.gz | 45.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/s1/1s18 ftp://data.pdbj.org/pub/pdb/validation_reports/s1/1s18 | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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Details | The biological assembly is a monomer |
-Components
#1: Protein | Mass: 37042.176 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: SHAPY / Plasmid: pET3a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)/pLysS / References: UniProt: Q8WVQ1, apyrase #2: Chemical | #3: Chemical | ChemComp-ACT / #4: Chemical | ChemComp-TRS / #5: Water | ChemComp-HOH / | |
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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: 2.29 Å3/Da / Density % sol: 45.81 % | |||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 5 Details: PEG MME 2000, sodium acetate, ammonium sulfate, strontium chloride, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 295.0K | |||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Method: vapor diffusion, hanging drop | |||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 0.98, 0.9794, 0.9790, 0.9687 | |||||||||||||||
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Oct 12, 2002 | |||||||||||||||
Radiation | Monochromator: GRAPHITE / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||
Radiation wavelength |
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Reflection | Resolution: 1.7→72.6 Å / Num. obs: 65632 / % possible obs: 95.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.5 % / Biso Wilson estimate: 16.3 Å2 / Rmerge(I) obs: 0.057 / Net I/σ(I): 14.3 | |||||||||||||||
Reflection shell | Resolution: 1.7→1.76 Å / Redundancy: 2.3 % / Rmerge(I) obs: 0.238 / Mean I/σ(I) obs: 3.5 / Num. unique all: 5489 / % possible all: 79.2 | |||||||||||||||
Reflection | *PLUS Highest resolution: 1.7 Å / % possible obs: 95.3 % | |||||||||||||||
Reflection shell | *PLUS % possible obs: 79.2 % |
-Processing
Software |
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Refinement | Method to determine structure: MAD / Resolution: 1.7→72.55 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.953 / SU B: 1.899 / SU ML: 0.063 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.104 / ESU R Free: 0.101 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 19.001 Å2
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Refinement step | Cycle: LAST / Resolution: 1.7→72.55 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.7→1.747 Å / Total num. of bins used: 20
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Refinement | *PLUS Highest resolution: 1.7 Å / Lowest resolution: 72.6 Å / % reflection Rfree: 5 % / Rfactor Rfree: 0.191 / Rfactor Rwork: 0.157 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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