+Open data
-Basic information
Entry | Database: PDB / ID: 2x6l | |||||||||
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Title | X-ray Structure of Macrophage Inflammatory Protein-1 beta | |||||||||
Components | C-C MOTIF CHEMOKINE 4 | |||||||||
Keywords | IMMUNE SYSTEM / INFLAMMATORY RESPONSE / CHEMOTAXIS | |||||||||
Function / homology | Function and homology information CCR1 chemokine receptor binding / positive regulation of natural killer cell chemotaxis / CCR5 chemokine receptor binding / CCR chemokine receptor binding / lymphocyte chemotaxis / positive regulation of calcium ion transport / eosinophil chemotaxis / chemokine-mediated signaling pathway / Chemokine receptors bind chemokines / chemokine activity ...CCR1 chemokine receptor binding / positive regulation of natural killer cell chemotaxis / CCR5 chemokine receptor binding / CCR chemokine receptor binding / lymphocyte chemotaxis / positive regulation of calcium ion transport / eosinophil chemotaxis / chemokine-mediated signaling pathway / Chemokine receptors bind chemokines / chemokine activity / establishment or maintenance of cell polarity / Interleukin-10 signaling / monocyte chemotaxis / negative regulation by host of viral transcription / cellular response to interleukin-1 / positive regulation of calcium-mediated signaling / neutrophil chemotaxis / cytokine activity / response to virus / response to toxic substance / cellular response to type II interferon / cell-cell signaling / cellular response to tumor necrosis factor / G alpha (i) signalling events / positive regulation of ERK1 and ERK2 cascade / cell adhesion / inflammatory response / immune response / G protein-coupled receptor signaling pathway / signal transduction / extracellular space / extracellular region / identical protein binding Similarity search - Function | |||||||||
Biological species | HOMO SAPIENS (human) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / OTHER / Resolution: 2.602 Å | |||||||||
Authors | Guo, Q. / Ren, M. / Tang, W. | |||||||||
Citation | Journal: Embo J. / Year: 2010 Title: Polymerization of Mip-1 Chemokine (Ccl3 and Ccl4) and Clearance of Mip-1 by Insulin-Degrading Enzyme. Authors: Ren, M. / Guo, Q. / Guo, L. / Lenz, M. / Qian, F. / Koenen, R.R. / Xu, H. / Schilling, A.B. / Weber, C. / Ye, R.D. / Dinner, A.R. / Tang, W. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2x6l.cif.gz | 74.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2x6l.ent.gz | 61.7 KB | Display | PDB format |
PDBx/mmJSON format | 2x6l.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2x6l_validation.pdf.gz | 460.3 KB | Display | wwPDB validaton report |
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Full document | 2x6l_full_validation.pdf.gz | 465.2 KB | Display | |
Data in XML | 2x6l_validation.xml.gz | 15.1 KB | Display | |
Data in CIF | 2x6l_validation.cif.gz | 21.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/x6/2x6l ftp://data.pdbj.org/pub/pdb/validation_reports/x6/2x6l | HTTPS FTP |
-Related 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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4 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 7824.742 Da / Num. of mol.: 5 / Source method: obtained synthetically / Source: (synth.) HOMO SAPIENS (human) / References: UniProt: P13236 #2: Chemical | #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 3.11 Å3/Da / Density % sol: 60.2 % / Description: NONE |
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-Data collection
Diffraction | Mean temperature: 287 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9792 |
Detector | Type: ADSC CCD / Detector: CCD / Date: Nov 1, 2001 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9792 Å / Relative weight: 1 |
Reflection | Resolution: 2.6→50 Å / Num. obs: 15529 / % possible obs: 100 % / Observed criterion σ(I): 1 / Redundancy: 7.2 % / Rmerge(I) obs: 0.12 / Net I/σ(I): 17.6 |
-Processing
Software | Name: PHENIX / Version: (PHENIX.REFINE) / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||
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Refinement | Method to determine structure: OTHER Starting model: NONE Resolution: 2.602→49.448 Å / SU ML: 0.31 / σ(F): 0.16 / Phase error: 24.09 / 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 / Bsol: 42.241 Å2 / ksol: 0.405 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||
Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 2.602→49.448 Å
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Refine LS restraints |
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LS refinement shell |
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