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Yorodumi- PDB-5e6w: Re-refinement of the Crystal Structure of the Plexin-Semaphorin-I... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5e6w | ||||||
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Title | Re-refinement of the Crystal Structure of the Plexin-Semaphorin-Integrin Domain/Hybrid Domain/I-EGF1 Segment from the Human Integrin b2 Subunit | ||||||
Components | Integrin beta-2 | ||||||
Keywords | CELL ADHESION / CD18 fragment | ||||||
Function / homology | Function and homology information integrin alphaX-beta2 complex / positive regulation of prostaglandin-E synthase activity / positive regulation of neutrophil degranulation / integrin alphaM-beta2 complex / integrin alphaL-beta2 complex / ICAM-3 receptor activity / complement component C3b binding / neutrophil migration / Toll Like Receptor 4 (TLR4) Cascade / negative regulation of dopamine metabolic process ...integrin alphaX-beta2 complex / positive regulation of prostaglandin-E synthase activity / positive regulation of neutrophil degranulation / integrin alphaM-beta2 complex / integrin alphaL-beta2 complex / ICAM-3 receptor activity / complement component C3b binding / neutrophil migration / Toll Like Receptor 4 (TLR4) Cascade / negative regulation of dopamine metabolic process / cell-cell adhesion via plasma-membrane adhesion molecules / heterotypic cell-cell adhesion / integrin complex / cellular response to low-density lipoprotein particle stimulus / positive regulation of leukocyte adhesion to vascular endothelial cell / leukocyte cell-cell adhesion / phagocytosis, engulfment / receptor clustering / amyloid-beta clearance / endodermal cell differentiation / plasma membrane raft / regulation of peptidyl-tyrosine phosphorylation / tertiary granule membrane / ficolin-1-rich granule membrane / positive regulation of protein targeting to membrane / Integrin cell surface interactions / specific granule membrane / positive regulation of superoxide anion generation / cell adhesion molecule binding / heat shock protein binding / neutrophil chemotaxis / receptor-mediated endocytosis / cell-matrix adhesion / integrin-mediated signaling pathway / Cell surface interactions at the vascular wall / cell-cell adhesion / microglial cell activation / receptor internalization / integrin binding / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / extracellular vesicle / cell-cell signaling / amyloid-beta binding / regulation of cell shape / Interleukin-4 and Interleukin-13 signaling / receptor complex / cell adhesion / inflammatory response / external side of plasma membrane / focal adhesion / Neutrophil degranulation / protein kinase binding / apoptotic process / cell surface / extracellular exosome / membrane / metal ion binding / plasma membrane Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.2 Å | ||||||
Authors | Springer, T.A. / Sen, M. | ||||||
Funding support | United States, 1items
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Citation | Journal: J. Biol. Chem. / Year: 2007 Title: A structural hypothesis for the transition between bent and extended conformations of the leukocyte beta2 integrins. Authors: Shi, M. / Foo, S.Y. / Tan, S.M. / Mitchell, E.P. / Law, S.K. / Lescar, J. | ||||||
History |
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Remark 0 | This entry 5E6W reflects an alternative modeling of the structural data in r2P28SF original data ...This entry 5E6W reflects an alternative modeling of the structural data in r2P28SF original data determined by Authors: Shi, M., Foo, S.Y., Tan, S.M., Mitchell, E.P., Law, S.K.A., Lescar, J. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5e6w.cif.gz | 141.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5e6w.ent.gz | 111 KB | Display | PDB format |
PDBx/mmJSON format | 5e6w.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5e6w_validation.pdf.gz | 447.2 KB | Display | wwPDB validaton report |
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Full document | 5e6w_full_validation.pdf.gz | 453.5 KB | Display | |
Data in XML | 5e6w_validation.xml.gz | 15.8 KB | Display | |
Data in CIF | 5e6w_validation.cif.gz | 22.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/e6/5e6w ftp://data.pdbj.org/pub/pdb/validation_reports/e6/5e6w | HTTPS FTP |
-Related structure data
Related structure data | 5e6rC 5e6sC 5e6uC 5e6vC 5e6xC 5es4C 1yukS 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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-Components
#1: Protein | Mass: 34898.453 Da / Num. of mol.: 1 / Fragment: UNP residues 23-122, 362-574 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: ITGB2, CD18, MFI7 / Production host: Homo sapiens (human) / References: UniProt: P05107 | ||
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#2: Sugar | #3: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.45 Å3/Da / Density % sol: 49.7 % / Description: AUTHOR USED THE SF DATA FROM ENTRY 2P28 |
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-Data collection
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
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Radiation wavelength | Relative weight: 1 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1YUK Resolution: 2.2→24.971 Å / SU ML: 0.32 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 26.41 / 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→24.971 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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