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Open data
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Basic information
Entry | Database: PDB / ID: 1m8a | ||||||
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Title | Human MIP-3alpha/CCL20 | ||||||
![]() | Small inducible cytokine A20 | ||||||
![]() | CYTOKINE / CC-chemokine / IL-8 type dimer | ||||||
Function / homology | ![]() thymocyte migration / CCR6 chemokine receptor binding / T cell migration / CCR chemokine receptor binding / lymphocyte chemotaxis / chemokine-mediated signaling pathway / Chemokine receptors bind chemokines / chemokine activity / Interleukin-10 signaling / monocyte chemotaxis ...thymocyte migration / CCR6 chemokine receptor binding / T cell migration / CCR chemokine receptor binding / lymphocyte chemotaxis / chemokine-mediated signaling pathway / Chemokine receptors bind chemokines / chemokine activity / Interleukin-10 signaling / monocyte chemotaxis / : / positive regulation of T cell migration / cellular response to interleukin-1 / neutrophil chemotaxis / cell chemotaxis / cellular response to type II interferon / chemotaxis / cell-cell signaling / cellular response to tumor necrosis factor / G alpha (i) signalling events / positive regulation of ERK1 and ERK2 cascade / defense response to bacterium / inflammatory response / immune response / G protein-coupled receptor signaling pathway / signal transduction / extracellular space / extracellular region Similarity search - Function | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Hoover, D.M. / Boulegue, C. / Yang, D. / Oppenheim, J.J. / Tucker, K. / Lu, W. / Lubkowski, J. | ||||||
![]() | ![]() Title: The structure of human macrophage inflammatory protein-3alpha /CCL20. Linking antimicrobial and CC chemokine receptor-6-binding activities with human beta-defensins Authors: Hoover, D.M. / Boulegue, C. / Yang, D. / Oppenheim, J.J. / Tucker, K. / Lu, W. / Lubkowski, J. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 39.6 KB | Display | ![]() |
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PDB format | ![]() | 31 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 453.8 KB | Display | ![]() |
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Full document | ![]() | 456.6 KB | Display | |
Data in XML | ![]() | 10 KB | Display | |
Data in CIF | ![]() | 13.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1eqtS 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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Unit cell |
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Details | The molecule is likely a monomer |
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Components
#1: Protein | Mass: 8043.568 Da / Num. of mol.: 2 / Source method: obtained synthetically Details: THE PROTEIN WAS SYNTHESIZED USING Machine-assisted stepwise solid phase peptide synthesis on an Applied Biosystems 433A synthesizer using a custom-designed program tailored from the ...Details: THE PROTEIN WAS SYNTHESIZED USING Machine-assisted stepwise solid phase peptide synthesis on an Applied Biosystems 433A synthesizer using a custom-designed program tailored from the published in situ neutralization/HBTU activation protocol for Boc chemistry (Schnolzer, M. et al. (1992) J.Pept.Protein Res. 40, 180-193). IT IS NATURALLY FOUND IN HOMO SAPIENS (HUMAN). References: UniProt: P78556 #2: Chemical | ChemComp-IPA / #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.69 Å3/Da / Density % sol: 54.3 % | ||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 285 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: isopropanol, sodium citrate, N-(2-hydroxyethyl)piperazine-N'-(2-ethanesulfonic acid), pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 285K | ||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 12 ℃ | ||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Jan 25, 2002 / Details: mirrors |
Radiation | Monochromator: si crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→20 Å / Num. all: 21953 / Num. obs: 21953 / % possible obs: 97.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.5 % / Rmerge(I) obs: 0.067 / Net I/σ(I): 23.8 |
Reflection shell | Resolution: 1.7→1.76 Å / Rmerge(I) obs: 0.623 / Mean I/σ(I) obs: 1.9 / % possible all: 96.8 |
Reflection | *PLUS Highest resolution: 1.7 Å / Lowest resolution: 20 Å / Num. measured all: 99101 |
Reflection shell | *PLUS Highest resolution: 1.7 Å / % possible obs: 96.8 % |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1EQT Resolution: 1.7→15 Å / Num. parameters: 4979 / Num. restraintsaints: 4435 Isotropic thermal model: anisotropic for sulfur, isotropic otherwise Cross valid method: FREE R / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber Details: ANISOTROPIC SCALING APPLIED BY THE METHOD OF PARKIN, MOEZZI & HOPE, J.APPL.CRYST.28(1995)53-56
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Solvent computation | Solvent model: MOEWS & KRETSINGER, J.MOL.BIOL.91(1973)201-228 | |||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 27.7 Å2 | |||||||||||||||||||||||||||||||||
Refine analyze | Num. disordered residues: 5 / Occupancy sum hydrogen: 0 / Occupancy sum non hydrogen: 1175 | |||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.7→15 Å
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Refine LS restraints |
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Software | *PLUS Name: SHELXL / Version: 97 / Classification: refinement | |||||||||||||||||||||||||||||||||
Refinement | *PLUS Lowest resolution: 15 Å / % reflection Rfree: 4 % / Rfactor all: 0.19 / Rfactor Rfree: 0.238 / Rfactor Rwork: 0.19 | |||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS Type: s_plane_restr / Dev ideal: 0.028 |