+Open data
-Basic information
Entry | Database: PDB / ID: 1o80 | ||||||
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Title | Crystal structure of IP-10 H-Form | ||||||
Components | SMALL INDUCIBLE CYTOKINE B10 | ||||||
Keywords | CHEMOKINE / INTERFERON INDUCTION / CHEMOTAXIS / INFLAMMATORY RESPONSE | ||||||
Function / homology | Function and homology information regulation of T cell chemotaxis / negative regulation of myoblast fusion / CXCR3 chemokine receptor binding / regulation of endothelial tube morphogenesis / cellular response to interleukin-17 / CXCR chemokine receptor binding / response to auditory stimulus / cAMP-dependent protein kinase regulator activity / negative regulation of myoblast differentiation / T cell chemotaxis ...regulation of T cell chemotaxis / negative regulation of myoblast fusion / CXCR3 chemokine receptor binding / regulation of endothelial tube morphogenesis / cellular response to interleukin-17 / CXCR chemokine receptor binding / response to auditory stimulus / cAMP-dependent protein kinase regulator activity / negative regulation of myoblast differentiation / T cell chemotaxis / response to vitamin D / positive regulation of monocyte chemotaxis / chemokine-mediated signaling pathway / blood circulation / Chemokine receptors bind chemokines / endothelial cell activation / chemokine activity / muscle organ development / chemoattractant activity / Interleukin-10 signaling / positive regulation of T cell migration / negative regulation of angiogenesis / antiviral innate immune response / neutrophil chemotaxis / positive regulation of release of sequestered calcium ion into cytosol / response to gamma radiation / adenylate cyclase-activating G protein-coupled receptor signaling pathway / cellular response to virus / chemotaxis / antimicrobial humoral immune response mediated by antimicrobial peptide / cell-cell signaling / heparin binding / regulation of cell population proliferation / cellular response to heat / G alpha (i) signalling events / cellular response to lipopolysaccharide / regulation of apoptotic process / cell surface receptor signaling pathway / inflammatory response / G protein-coupled receptor signaling pathway / external side of plasma membrane / signaling receptor binding / positive regulation of cell population proliferation / signal transduction / positive regulation of transcription by RNA polymerase II / extracellular space / extracellular region Similarity search - Function | ||||||
Biological species | HOMO SAPIENS (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å | ||||||
Authors | Swaminathan, G.J. / Holloway, D.E. / Papageorgiou, A.C. / Acharya, K.R. | ||||||
Citation | Journal: Structure / Year: 2003 Title: Crystal Structures of Oligomeric Forms of the Ip-10/Cxcl10 Chemokine Authors: Swaminathan, G.J. / Holloway, D.E. / Colvin, R.A. / Campanella, G.K. / Papageorgiou, A.C. / Luster, A.D. / Acharya, K.R. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1o80.cif.gz | 40.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1o80.ent.gz | 29 KB | Display | PDB format |
PDBx/mmJSON format | 1o80.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1o80_validation.pdf.gz | 369.8 KB | Display | wwPDB validaton report |
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Full document | 1o80_full_validation.pdf.gz | 372.8 KB | Display | |
Data in XML | 1o80_validation.xml.gz | 4.8 KB | Display | |
Data in CIF | 1o80_validation.cif.gz | 6.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/o8/1o80 ftp://data.pdbj.org/pub/pdb/validation_reports/o8/1o80 | HTTPS FTP |
-Related structure data
Related structure data | 1o7yC 1o7zC 1rhpS C: citing same article (ref.) 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
#1: Protein | Mass: 8637.345 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) HOMO SAPIENS (human) / References: UniProt: P02778 #2: Water | ChemComp-HOH / | Compound details | CHEMOTACTIC FOR MONOCYTES AND T LYMPHOCYTES. BINDS TO CXCR3. INDUCED BY INTERFERON GAMMA. A DIVERSE ...CHEMOTACTI | Sequence details | THE SEQUENCE CONFLICT INDICATED IN THE SEQADV RECORDS ARISES FROM A DIFFERENCE IN THE PRIMARY ...THE SEQUENCE CONFLICT INDICATED IN THE SEQADV RECORDS ARISES FROM A DIFFERENCE | |
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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: 3.5 Å3/Da / Density % sol: 64.6 % | ||||||||||||||||||||||||
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Crystal grow | pH: 8.75 Details: 10MG/ML PROTEIN, 0.1M TRIS-HCL BUFFER, PH 8.75, 3.3M SODIUM FORMATE | ||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 16 ℃ / Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||
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: SRS / Beamline: PX14.1 / Wavelength: 1.488 |
Detector | Type: ADSC CCD / Detector: CCD / Date: Feb 25, 2002 / Details: MIRRORS |
Radiation | Monochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.488 Å / Relative weight: 1 |
Reflection | Resolution: 2→50 Å / Num. obs: 17139 / % possible obs: 98.4 % / Redundancy: 12.8 % / Biso Wilson estimate: 50.9 Å2 / Rmerge(I) obs: 0.078 / Net I/σ(I): 20.1 |
Reflection shell | Resolution: 2→2.07 Å / Rmerge(I) obs: 0.52 / Mean I/σ(I) obs: 3.3 / % possible all: 99.8 |
Reflection | *PLUS Highest resolution: 2 Å / Lowest resolution: 50 Å / Num. measured all: 219378 |
Reflection shell | *PLUS % possible obs: 99.8 % / Rmerge(I) obs: 0.52 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1RHP Resolution: 2→34.94 Å / Rfactor Rfree error: 0.01 / Data cutoff high absF: 505207.81 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 53.5519 Å2 / ksol: 0.363358 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 54.4 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2→34.94 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2→2.07 Å / Rfactor Rfree error: 0.056 / Total num. of bins used: 10
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Xplor file |
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Refinement | *PLUS Lowest resolution: 35 Å / % reflection Rfree: 6 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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