+Open data
-Basic information
Entry | Database: PDB / ID: 1esr | |||||||||
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Title | CRYSTAL STRUCTURE OF HUMAN MONOCYTE CHEMOTACTIC PROTEIN-2 | |||||||||
Components | MONOCYTE CHEMOTACTIC PROTEIN 2 | |||||||||
Keywords | CYTOKINE / CHEMOKINE / MONOCYTE CHEMOATTRACTANT PROTEIN / HIV-1 / PYROGLUTAMIC ACID | |||||||||
Function / homology | Function and homology information CCR2 chemokine receptor binding / negative regulation of leukocyte proliferation / negative regulation by host of viral genome replication / CCR chemokine receptor binding / lymphocyte chemotaxis / eosinophil chemotaxis / chemokine-mediated signaling pathway / chemokine activity / positive regulation of leukocyte migration / phospholipase activator activity ...CCR2 chemokine receptor binding / negative regulation of leukocyte proliferation / negative regulation by host of viral genome replication / CCR chemokine receptor binding / lymphocyte chemotaxis / eosinophil chemotaxis / chemokine-mediated signaling pathway / chemokine activity / positive regulation of leukocyte migration / phospholipase activator activity / exocytosis / monocyte chemotaxis / cellular response to interleukin-1 / neutrophil chemotaxis / response to virus / cellular response to type II interferon / intracellular calcium ion homeostasis / calcium ion transport / chemotaxis / cell-cell signaling / cellular response to tumor necrosis factor / heparin binding / angiogenesis / positive regulation of ERK1 and ERK2 cascade / protein kinase activity / inflammatory response / G protein-coupled receptor signaling pathway / signal transduction / extracellular space Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å | |||||||||
Authors | Blaszczyk, J. / Ji, X. | |||||||||
Citation | Journal: Biochemistry / Year: 2000 Title: Complete crystal structure of monocyte chemotactic protein-2, a CC chemokine that interacts with multiple receptors. Authors: Blaszczyk, J. / Coillie, E.V. / Proost, P. / Damme, J.V. / Opdenakker, G. / Bujacz, G.D. / Wang, J.M. / Ji, X. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1esr.cif.gz | 31.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1esr.ent.gz | 19.7 KB | Display | PDB format |
PDBx/mmJSON format | 1esr.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1esr_validation.pdf.gz | 417.9 KB | Display | wwPDB validaton report |
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Full document | 1esr_full_validation.pdf.gz | 420 KB | Display | |
Data in XML | 1esr_validation.xml.gz | 7.1 KB | Display | |
Data in CIF | 1esr_validation.cif.gz | 8.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/es/1esr ftp://data.pdbj.org/pub/pdb/validation_reports/es/1esr | HTTPS FTP |
-Related structure data
Related structure data | 1dokS S: Starting model for refinement |
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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 on special symmetry positions |
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-Components
#1: Protein | Mass: 8911.384 Da / Num. of mol.: 1 / Mutation: Q24(PCA) AND K69Q Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Plasmid: PHEN1 / Production host: Escherichia coli (E. coli) / Strain (production host): JM83 / References: UniProt: P80075 |
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#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.6 Å3/Da / Density % sol: 63 % | |||||||||||||||||||||||||
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Crystal grow | Temperature: 292 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: Ammonium sulfate, Tris-HCl, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 292K | |||||||||||||||||||||||||
Crystal grow | *PLUS Details: drop consists of equal amounts of protein and reservoir solutions | |||||||||||||||||||||||||
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: NSLS / Beamline: X9B / Wavelength: 0.97132 |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Nov 21, 1998 / Details: Mirror |
Radiation | Monochromator: Silicon 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97132 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→20 Å / Num. all: 10447 / Num. obs: 10447 / % possible obs: 98.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.1 % / Biso Wilson estimate: 32.2 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 19.7 |
Reflection shell | Resolution: 1.9→1.93 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.507 / Mean I/σ(I) obs: 1.7854 / Num. unique all: 469 / % possible all: 92.7 |
Reflection | *PLUS Num. obs: 9060 / % possible obs: 99 % / Num. measured all: 38808 / Rmerge(I) obs: 0.056 |
Reflection shell | *PLUS % possible obs: 97.6 % / Rmerge(I) obs: 0.39 / Mean I/σ(I) obs: 3.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1DOK Resolution: 2→20 Å / Num. parameters: 2793 / Num. restraintsaints: 2572 / Cross valid method: FREE R / σ(F): 0 / σ(I): 2 / Stereochemistry target values: ENGH AND HUBER Details: Least-squares refinement using the Konnert-Hendrickson conjugate-gradient algorithm
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Solvent computation | Solvent model: Moews & Kretsinger, J. Mol. Biol. 91 (1975) 201-228 | |||||||||||||||||||||||||||||||||
Refine analyze | Num. disordered residues: 1 / Occupancy sum hydrogen: 0 / Occupancy sum non hydrogen: 711 | |||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2→20 Å
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Refine LS restraints |
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Software | *PLUS Name: SHELXL-97 / Classification: refinement | |||||||||||||||||||||||||||||||||
Refinement | *PLUS | |||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS Biso mean: 49.2 Å2 |