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Yorodumi- PDB-1qe6: INTERLEUKIN-8 WITH AN ADDED DISULFIDE BETWEEN RESIDUES 5 AND 33 (... -
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-Basic information
Entry | Database: PDB / ID: 1qe6 | ||||||
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Title | INTERLEUKIN-8 WITH AN ADDED DISULFIDE BETWEEN RESIDUES 5 AND 33 (L5C/H33C) | ||||||
Components | INTERLEUKIN-8 VARIANT | ||||||
Keywords | IMMUNE SYSTEM / INTERCRINE ALPHA FAMILY | ||||||
Function / homology | Function and homology information regulation of single stranded viral RNA replication via double stranded DNA intermediate / regulation of entry of bacterium into host cell / interleukin-8 receptor binding / positive regulation of cellular biosynthetic process / negative regulation of cell adhesion molecule production / negative regulation of G protein-coupled receptor signaling pathway / ATF4 activates genes in response to endoplasmic reticulum stress / CXCR chemokine receptor binding / embryonic digestive tract development / neutrophil activation ...regulation of single stranded viral RNA replication via double stranded DNA intermediate / regulation of entry of bacterium into host cell / interleukin-8 receptor binding / positive regulation of cellular biosynthetic process / negative regulation of cell adhesion molecule production / negative regulation of G protein-coupled receptor signaling pathway / ATF4 activates genes in response to endoplasmic reticulum stress / CXCR chemokine receptor binding / embryonic digestive tract development / neutrophil activation / induction of positive chemotaxis / cellular response to fibroblast growth factor stimulus / positive regulation of neutrophil chemotaxis / chemokine-mediated signaling pathway / Chemokine receptors bind chemokines / chemokine activity / Interleukin-10 signaling / cellular response to interleukin-1 / regulation of cell adhesion / response to endoplasmic reticulum stress / Peptide ligand-binding receptors / neutrophil chemotaxis / calcium-mediated signaling / response to molecule of bacterial origin / receptor internalization / positive regulation of angiogenesis / chemotaxis / antimicrobial humoral immune response mediated by antimicrobial peptide / heparin binding / cellular response to tumor necrosis factor / G alpha (i) signalling events / Senescence-Associated Secretory Phenotype (SASP) / angiogenesis / Interleukin-4 and Interleukin-13 signaling / cellular response to lipopolysaccharide / intracellular signal transduction / inflammatory response / G protein-coupled receptor signaling pathway / negative regulation of cell population proliferation / negative regulation of gene expression / positive regulation of gene expression / signal transduction / extracellular space / extracellular region Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.35 Å | ||||||
Authors | Gerber, N. / Lowman, H. / Artis, D.R. / Eigenbrot, C. | ||||||
Citation | Journal: Proteins / Year: 2000 Title: Receptor-binding conformation of the "ELR" motif of IL-8: X-ray structure of the L5C/H33C variant at 2.35 A resolution. Authors: Gerber, N. / Lowman, H. / Artis, D.R. / Eigenbrot, C. #1: Journal: Proc.Natl.Acad.Sci.USA / Year: 1991 Title: Crystal structure of IL-8:Symbiosis of NMR and crystallography Authors: Baldwin, E.T. / Weber, I.T. / Charles, R.St. / Xuan, J.-C. #2: Journal: Proteins / Year: 1997 Title: Structural change and receptor binding in a chemokine mutant with a re- arranged disulfide: X-ray structure of E38C/C50A IL-8 at 2 A resolution. Authors: Eigenbrot, C. / Lowman, H.B. / Chee, L. / Artis, D.R. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1qe6.cif.gz | 67.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1qe6.ent.gz | 54.8 KB | Display | PDB format |
PDBx/mmJSON format | 1qe6.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qe/1qe6 ftp://data.pdbj.org/pub/pdb/validation_reports/qe/1qe6 | HTTPS FTP |
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-Related structure data
Related structure data | |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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3 |
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Unit cell |
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-Components
#1: Protein | Mass: 8356.787 Da / Num. of mol.: 4 / Mutation: L5C, H33C Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Cell: MONOCYTE / Production host: Escherichia coli (E. coli) / References: UniProt: P10145 #2: Chemical | #3: 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: 2.33 Å3/Da / Density % sol: 47.22 % | ||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 292 K / Method: vapor diffusion, hanging drop / pH: 6.2 Details: NACL, AMMONIUM SULFATE, PEG 8000, pH 6.2, VAPOR DIFFUSION, HANGING DROP, temperature 19K | ||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 20 ℃ | ||||||||||||||||||||||||||||||||||||||||||||||||
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: CHESS / Beamline: A1 / Wavelength: 0.908 |
Detector | Type: PRINCETON 1K / Detector: CCD / Date: Oct 15, 1996 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.908 Å / Relative weight: 1 |
Reflection | Resolution: 2.35→50 Å / Num. all: 12843 / Num. obs: 12188 / % possible obs: 95 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.3 % / Biso Wilson estimate: 22.4 Å2 / Rmerge(I) obs: 0.088 / Net I/σ(I): 13 |
Reflection shell | Resolution: 2.35→2.43 Å / Redundancy: 2.1 % / Rmerge(I) obs: 0.113 / % possible all: 86 |
-Processing
Software |
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Refinement | Resolution: 2.35→20 Å / Rfactor Rfree error: 0.009 / Data cutoff high absF: 100000 / Data cutoff low absF: 0.1 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 999.999 / Stereochemistry target values: ENGH AND HUBER
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Displacement parameters | Biso mean: 10.1 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.35→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.35→2.43 Å / Rfactor Rfree error: 0.033 / Total num. of bins used: 10
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Xplor file |
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Software | *PLUS Name: X-PLOR(ONLINE) / Version: 3.851 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS σ(F): 2 / % reflection Rfree: 7.2 % / Rfactor obs: 0.206 / Rfactor Rfree: 0.277 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS Biso mean: 10.1 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor Rfree: 0.387 / % reflection Rfree: 12.6 % / Rfactor Rwork: 0.216 |