+Open data
-Basic information
Entry | Database: PDB / ID: 4db5 | ||||||
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Title | Crystal structure of Rabbit GITRL | ||||||
Components | Tumor necrosis factor ligand superfamily member 18 | ||||||
Keywords | IMMUNE SYSTEM / GITRL / GLUCOCORTICOID-INDUCED TNF RECEPTOR LIGAND / TNFRSF18 / Structural genomics / PSI-Biology / New York Structural Genomics Research Consortium / NYSGRC / Atoms-to-Animals: The Immune Function Network / IFN | ||||||
Function / homology | Function and homology information tumor necrosis factor receptor superfamily binding / positive regulation of leukocyte migration / 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 / membrane => GO:0016020 / identical protein binding Similarity search - Function | ||||||
Biological species | Oryctolagus cuniculus (rabbit) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.522 Å | ||||||
Authors | Kumar, P.R. / Bhosle, R. / Gizzi, A. / Scott Glenn, A. / Chowhury, S. / Hillerich, B. / Seidel, R. / Nathenson, S.G. / Almo, S.C. / New York Structural Genomics Research Consortium (NYSGRC) / Atoms-to-Animals: The Immune Function Network (IFN) | ||||||
Citation | Journal: to be published Title: Crystal structure of GITRL from Oryctolagus cuniculus Authors: Kumar, P.R. / Bhosle, R. / Gizzi, A. / Scott Glenn, A. / Chowhury, S. / Hillerich, B. / Seidel, R. / 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 | 4db5.cif.gz | 69.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4db5.ent.gz | 51.3 KB | Display | PDB format |
PDBx/mmJSON format | 4db5.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4db5_validation.pdf.gz | 686.9 KB | Display | wwPDB validaton report |
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Full document | 4db5_full_validation.pdf.gz | 687.5 KB | Display | |
Data in XML | 4db5_validation.xml.gz | 8.6 KB | Display | |
Data in CIF | 4db5_validation.cif.gz | 11.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/db/4db5 ftp://data.pdbj.org/pub/pdb/validation_reports/db/4db5 | HTTPS FTP |
-Related structure data
Related structure data | 3fc0S S: Starting model for refinement |
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Similar structure data | |
Other databases |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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Components on special symmetry positions |
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Details | The biological assembly is a trimer generated from the monomer in the asymmetric unit by crystallographic symmetry operations |
-Components
#1: Protein | Mass: 14055.084 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Oryctolagus cuniculus (rabbit) / Gene: GITRL, TNFSF18 / Plasmid: pET28b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: G1TIM1 |
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#2: Chemical | ChemComp-B3P / |
#3: 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: 3.04 Å3/Da / Density % sol: 59.53 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7 Details: Protein (20 mM Hepes, pH 7.5, 150 mM NaCl, 10% glycerol; Reservoir (0.1M Bis-Tris Propane pH 7.0, 2.4M DL-Malic acid); Cryoprotection (Reservoir + 30% glycerol), Sitting Drop, Vapor ...Details: Protein (20 mM Hepes, pH 7.5, 150 mM NaCl, 10% glycerol; Reservoir (0.1M Bis-Tris Propane pH 7.0, 2.4M DL-Malic acid); Cryoprotection (Reservoir + 30% glycerol), Sitting Drop, Vapor Diffusion, temperature 298K, VAPOR DIFFUSION, SITTING DROP |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.075 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Sep 27, 2011 / Details: MIRRORS | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1.075 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.52→50 Å / Num. obs: 26128 / % possible obs: 100 % / Redundancy: 33.1 % / Rmerge(I) obs: 0.051 / Χ2: 1.044 / Net I/σ(I): 12.5 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: pdb entry 3FC0 Resolution: 1.522→29.147 Å / Occupancy max: 1 / Occupancy min: 0.21 / FOM work R set: 0.9095 / SU ML: 0.16 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 15.63 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.98 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 53.362 Å2 / ksol: 0.442 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 57.92 Å2 / Biso mean: 16.9381 Å2 / Biso min: 7.42 Å2
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Refinement step | Cycle: LAST / Resolution: 1.522→29.147 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 10 / % reflection obs: 100 %
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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