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Yorodumi- PDB-3fc0: 1.8 A crystal structure of murine GITR ligand dimer expressed in ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3fc0 | ||||||
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Title | 1.8 A crystal structure of murine GITR ligand dimer expressed in Drosophila melanogaster S2 cells | ||||||
Components | GITR ligand | ||||||
Keywords | PROTEIN BINDING / GITRL / Glucocorticoid-Induced TNF Receptor Ligand / Receptor | ||||||
Function / homology | Function and homology information regulation of dendritic cell chemotaxis / negative regulation of T-helper 17 cell lineage commitment / TNFs bind their physiological receptors / tumor necrosis factor receptor superfamily binding / tumor necrosis factor receptor binding / positive regulation of monocyte chemotaxis / regulation of T cell proliferation / positive regulation of macrophage chemotaxis / positive regulation of cell adhesion / regulation of protein-containing complex assembly ...regulation of dendritic cell chemotaxis / negative regulation of T-helper 17 cell lineage commitment / TNFs bind their physiological receptors / tumor necrosis factor receptor superfamily binding / tumor necrosis factor receptor binding / positive regulation of monocyte chemotaxis / regulation of T cell proliferation / positive regulation of macrophage chemotaxis / positive regulation of cell adhesion / regulation of protein-containing complex assembly / T cell proliferation involved in immune response / tumor necrosis factor-mediated signaling pathway / cytokine activity / positive regulation of inflammatory response / positive regulation of NF-kappaB transcription factor activity / adaptive immune response / cell surface / extracellular space / identical protein binding / plasma membrane Similarity search - Function | ||||||
Biological species | Mus musculus (house mouse) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.76 Å | ||||||
Authors | Chattopadhyay, K. / Ramagopal, U.A. / Nathenson, S.G. / Almo, S.C. | ||||||
Citation | Journal: Acta Crystallogr.,Sect.D / Year: 2009 Title: 1.8 A structure of murine GITR ligand dimer expressed in Drosophila melanogaster S2 cells. Authors: Chattopadhyay, K. / Ramagopal, U.A. / Nathenson, S.G. / Almo, S.C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3fc0.cif.gz | 63.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3fc0.ent.gz | 45.4 KB | Display | PDB format |
PDBx/mmJSON format | 3fc0.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3fc0_validation.pdf.gz | 451.3 KB | Display | wwPDB validaton report |
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Full document | 3fc0_full_validation.pdf.gz | 456.6 KB | Display | |
Data in XML | 3fc0_validation.xml.gz | 12.2 KB | Display | |
Data in CIF | 3fc0_validation.cif.gz | 16 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fc/3fc0 ftp://data.pdbj.org/pub/pdb/validation_reports/fc/3fc0 | HTTPS FTP |
-Related structure data
Related structure data | 2qdnS 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: 15902.297 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Gene: Tnfsf18, Gitrl / Plasmid: pMT-BIP-V5-HIS / Production host: Drosophila melanogaster (fruit fly) / Strain (production host): S2 cells / References: UniProt: Q7TS55 #2: Chemical | ChemComp-ACT / | #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: 2.12 Å3/Da / Density % sol: 41.99 % |
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Crystal grow | Temperature: 298 K / pH: 7 Details: 15% Tacsimate pH 7.0, 0.1M Hepes, 2% PEG 3350, Vapor diffusion, Sitting drop, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 0.979 |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 14, 2008 |
Radiation | Protocol: SINGLE WAVELENGTH / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 1.76→30 Å / Num. obs: 27086 / % possible obs: 99.3 % / Redundancy: 7.7 % / Biso Wilson estimate: 24.86 Å2 / Rmerge(I) obs: 0.058 / Rsym value: 0.052 |
Reflection shell | Resolution: 1.76→1.82 Å / Redundancy: 6.6 % / Rmerge(I) obs: 0.278 / Mean I/σ(I) obs: 6.2 / Rsym value: 0.204 / % possible all: 93.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2QDN Resolution: 1.76→30 Å / Cor.coef. Fo:Fc: 0.941 / Cor.coef. Fo:Fc free: 0.929 / Occupancy max: 1 / Occupancy min: 1 / SU B: 2.727 / SU ML: 0.089 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.137 / ESU R Free: 0.132 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES: REFINED INDIVIDUALLY
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 30.95 Å2
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Refinement step | Cycle: LAST / Resolution: 1.76→30 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.76→1.8 Å / Total num. of bins used: 20
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