+Open data
-Basic information
Entry | Database: PDB / ID: 1g1q | ||||||
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Title | Crystal structure of P-selectin lectin/EGF domains | ||||||
Components | P-SELECTIN | ||||||
Keywords | IMMUNE SYSTEM / MEMBRANE PROTEIN / Lectin / EGF / Adhesion molecule | ||||||
Function / homology | Function and homology information regulation of integrin activation / fucose binding / platelet dense granule membrane / glycosphingolipid binding / positive regulation of leukocyte tethering or rolling / sialic acid binding / oligosaccharide binding / platelet alpha granule membrane / calcium-dependent cell-cell adhesion via plasma membrane cell adhesion molecules / leukocyte tethering or rolling ...regulation of integrin activation / fucose binding / platelet dense granule membrane / glycosphingolipid binding / positive regulation of leukocyte tethering or rolling / sialic acid binding / oligosaccharide binding / platelet alpha granule membrane / calcium-dependent cell-cell adhesion via plasma membrane cell adhesion molecules / leukocyte tethering or rolling / positive regulation of platelet activation / positive regulation of leukocyte migration / heterophilic cell-cell adhesion via plasma membrane cell adhesion molecules / leukocyte cell-cell adhesion / response to cytokine / Cell surface interactions at the vascular wall / lipopolysaccharide binding / cell-cell adhesion / integrin binding / calcium-dependent protein binding / Platelet degranulation / heparin binding / defense response to Gram-negative bacterium / response to lipopolysaccharide / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / cell adhesion / inflammatory response / external side of plasma membrane / calcium ion binding / extracellular space / plasma membrane Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.4 Å | ||||||
Authors | Somers, W.S. / Camphausen, R.T. | ||||||
Citation | Journal: Cell(Cambridge,Mass.) / Year: 2000 Title: Insights into the molecular basis of leukocyte tethering and rolling revealed by structures of P- and E-selectin bound to SLe(X) and PSGL-1. Authors: Somers, W.S. / Tang, J. / Shaw, G.D. / Camphausen, R.T. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1g1q.cif.gz | 139.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1g1q.ent.gz | 116.4 KB | Display | PDB format |
PDBx/mmJSON format | 1g1q.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1g1q_validation.pdf.gz | 399.8 KB | Display | wwPDB validaton report |
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Full document | 1g1q_full_validation.pdf.gz | 412.7 KB | Display | |
Data in XML | 1g1q_validation.xml.gz | 15.3 KB | Display | |
Data in CIF | 1g1q_validation.cif.gz | 23.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/g1/1g1q ftp://data.pdbj.org/pub/pdb/validation_reports/g1/1g1q | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 19131.238 Da / Num. of mol.: 4 / Fragment: LECTIN/EGF DOMAINS Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Cell (production host): ovary [CHO] cells / Production host: Cricetulus griseus (Chinese hamster) / References: UniProt: P16109 #2: Chemical | ChemComp-CA / #3: Chemical | #4: 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: 2.86 Å3/Da / Density % sol: 57 % | ||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: Tris-HCl, NaCl, CaCl2, 2-methyl-2,4-pentanediol, PEG 6000, pH 8.5, VAPOR DIFFUSION, HANGING DROP at 291K | ||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 18 ℃ / Method: vapor diffusion | ||||||||||||||||||||||||||||||||||||||||||
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 RU200 / Wavelength: 1.5418 Å |
Detector | Type: RIGAKU RAXIS II / Detector: IMAGE PLATE / Date: Jan 1, 1995 / Details: Yale/MSC mirrors |
Radiation | Monochromator: Mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.4→15 Å / Num. all: 32570 / Num. obs: 32570 / % possible obs: 95.8 % / Observed criterion σ(F): 3 / Observed criterion σ(I): 3 / Redundancy: 7.3798 % / Biso Wilson estimate: 20 Å2 / Rmerge(I) obs: 0.052 / Net I/σ(I): 35.7 |
Reflection shell | Resolution: 2.4→2.49 Å / Redundancy: 7.3798 % / Rmerge(I) obs: 0.225 / % possible all: 74.2 |
Reflection | *PLUS Num. measured all: 240361 |
Reflection shell | *PLUS % possible obs: 74.2 % / Mean I/σ(I) obs: 6.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.4→14 Å / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
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Refinement step | Cycle: LAST / Resolution: 2.4→14 Å
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Refine LS restraints |
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Software | *PLUS Name: CNS / Classification: refinement | |||||||||||||||||||||||||
Refinement | *PLUS Highest resolution: 2.4 Å / Lowest resolution: 14 Å / σ(F): 0 / % reflection Rfree: 5 % | |||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||
Displacement parameters | *PLUS |