+Open data
-Basic information
Entry | Database: PDB / ID: 2q1m | ||||||
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Title | Crystal Structure of human GITRL | ||||||
Components | Tumor necrosis factor ligand superfamily member 18 | ||||||
Keywords | SIGNALING PROTEIN / GITRL / Glucocorticoid-Induced TNF Receptor Ligand | ||||||
Function / homology | Function and homology information tumor necrosis factor receptor superfamily binding / TNFs bind their physiological receptors / positive regulation of leukocyte migration / regulation of T cell proliferation / positive regulation of cell adhesion / T cell proliferation involved in immune response / positive regulation of tyrosine phosphorylation of STAT protein / tumor necrosis factor-mediated signaling pathway / cytokine activity / cell-cell signaling ...tumor necrosis factor receptor superfamily binding / TNFs bind their physiological receptors / positive regulation of leukocyte migration / regulation of T cell proliferation / positive regulation of cell adhesion / T cell proliferation involved in immune response / positive regulation of tyrosine phosphorylation of STAT protein / tumor necrosis factor-mediated signaling pathway / cytokine activity / cell-cell signaling / positive regulation of NF-kappaB transcription factor activity / adaptive immune response / signaling receptor binding / negative regulation of apoptotic process / cell surface / signal transduction / extracellular space / identical protein binding / plasma membrane Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.3 Å | ||||||
Authors | Chattopadhyay, K. / Ramagopal, U.A. / Nathenson, S.G. / Almo, S.C. | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2007 Title: Assembly and structural properties of glucocorticoid-induced TNF receptor ligand: Implications for function. Authors: Chattopadhyay, K. / Ramagopal, U.A. / Mukhopadhaya, A. / Malashkevich, V.N. / Dilorenzo, T.P. / 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 | 2q1m.cif.gz | 33.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2q1m.ent.gz | 25.1 KB | Display | PDB format |
PDBx/mmJSON format | 2q1m.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2q1m_validation.pdf.gz | 425.9 KB | Display | wwPDB validaton report |
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Full document | 2q1m_full_validation.pdf.gz | 426.8 KB | Display | |
Data in XML | 2q1m_validation.xml.gz | 7.1 KB | Display | |
Data in CIF | 2q1m_validation.cif.gz | 8.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/q1/2q1m ftp://data.pdbj.org/pub/pdb/validation_reports/q1/2q1m | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Details | The biological unit is a trimer |
-Components
#1: Protein | Mass: 14687.742 Da / Num. of mol.: 1 / Fragment: Extracellular, TNF homology domain Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: TNFSF18, AITRL, GITRL, TL6 / Plasmid: pET-14b / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta (DE3) pLysS / References: UniProt: Q9UNG2 |
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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: 2.76 Å3/Da / Density % sol: 55.37 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 4.5 Details: 25% PEG 3350, 0.1 M Sodium Acetate pH 4.5, Vapor diffusion, Sitting drop, temperature 298K |
-Data collection
Diffraction |
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Diffraction source |
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Detector |
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Radiation |
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Radiation wavelength |
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Reflection | Redundancy: 16.9 % / Av σ(I) over netI: 6.1 / Number: 180253 / Rmerge(I) obs: 0.12 / Χ2: 1.05 / D res high: 2.5 Å / D res low: 50 Å / Num. obs: 10652 / % possible obs: 100 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Diffraction reflection shell |
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Reflection | Resolution: 2.3→21.7 Å / Num. all: 7131 / Num. obs: 7131 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 10.8 % / Rmerge(I) obs: 0.071 / Χ2: 1.296 / Net I/σ(I): 10.5 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Resolution: 2.3→2.38 Å / Redundancy: 10.8 % / Num. unique all: 693 / Χ2: 1.029 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 2.3→21.7 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.92 / SU B: 6.671 / SU ML: 0.164 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.299 / ESU R Free: 0.23 / 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: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 44.57 Å2
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Refinement step | Cycle: LAST / Resolution: 2.3→21.7 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.304→2.363 Å / Total num. of bins used: 20
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