+Open data
-Basic information
Entry | Database: PDB / ID: 2qdn | ||||||
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Title | Crystal Structure of mouse GITRL | ||||||
Components | GITR ligand | ||||||
Keywords | IMMUNE SYSTEM / GITRL / Glucocorticoid-Induced TNF Receptor Ligand | ||||||
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 / SAD / Resolution: 2.09 Å | ||||||
Authors | Chattopadhyay, K. / Ramagopal, U.A. / Nathenson, S.G. / Almo, S.C. | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.Usa / Year: 2008 Title: Evolution of GITRL immune function: murine GITRL exhibits unique structural and biochemical properties within the TNF superfamily. Authors: Chattopadhyay, K. / Ramagopal, U.A. / Brenowitz, M. / 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 | 2qdn.cif.gz | 62.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2qdn.ent.gz | 49.8 KB | Display | PDB format |
PDBx/mmJSON format | 2qdn.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2qdn_validation.pdf.gz | 430.5 KB | Display | wwPDB validaton report |
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Full document | 2qdn_full_validation.pdf.gz | 431.7 KB | Display | |
Data in XML | 2qdn_validation.xml.gz | 13.3 KB | Display | |
Data in CIF | 2qdn_validation.cif.gz | 19 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qd/2qdn ftp://data.pdbj.org/pub/pdb/validation_reports/qd/2qdn | HTTPS FTP |
-Related 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: 15011.407 Da / Num. of mol.: 2 / Fragment: TNF homology domain (Residues 46-173) Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Gene: Gitrl / Plasmid: pET-14b / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta (DE3) pLysS / References: UniProt: Q7TS55 #2: 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: 2.21 Å3/Da / Density % sol: 44.36 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7 Details: 15% PEG 3350, 0.1 M Succinic acid pH 7.0, Vapor diffusion, Sitting drop, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 1.74332 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: May 1, 2006 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1.74332 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Redundancy: 11.2 % / Av σ(I) over netI: 27.3 / Number: 309693 / Rmerge(I) obs: 0.043 / Χ2: 1.15 / D res high: 2.09 Å / D res low: 50 Å / Num. obs: 27694 / % possible obs: 90.3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Diffraction reflection shell |
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Reflection | Resolution: 2.09→50.06 Å / Num. all: 14872 / Num. obs: 14872 / % possible obs: 90.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 11.2 % / Rmerge(I) obs: 0.043 / Rsym value: 0.048 / Χ2: 1.154 / Net I/σ(I): 27.3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 2.09→50.06 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.923 / SU B: 4.305 / SU ML: 0.119 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.254 / ESU R Free: 0.201 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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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: 21.558 Å2
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Refinement step | Cycle: LAST / Resolution: 2.09→50.06 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.09→2.139 Å / Total num. of bins used: 20
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