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- PDB-2qdn: Crystal Structure of mouse GITRL -

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Basic information

Entry
Database: PDB / ID: 2qdn
TitleCrystal Structure of mouse GITRL
ComponentsGITR ligand
KeywordsIMMUNE 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 / positive regulation of leukocyte migration / positive regulation of macrophage chemotaxis / regulation of T cell proliferation / T cell proliferation involved in immune response ...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 / positive regulation of leukocyte migration / positive regulation of macrophage chemotaxis / regulation of T cell proliferation / T cell proliferation involved in immune response / positive regulation of cell adhesion / regulation of protein-containing complex assembly / positive regulation of tyrosine phosphorylation of STAT protein / 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
Tumor necrosis factor ligand superfamily member 18 / TNF(Tumour Necrosis Factor) family / Tumour necrosis factor domain / Jelly Rolls - #40 / Tumour necrosis factor-like domain superfamily / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
Tumor necrosis factor ligand superfamily member 18
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.09 Å
AuthorsChattopadhyay, K. / Ramagopal, U.A. / Nathenson, S.G. / Almo, S.C.
CitationJournal: 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
DepositionJun 21, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 1, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.2Oct 18, 2017Group: Refinement description / Category: software

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: GITR ligand
B: GITR ligand


Theoretical massNumber of molelcules
Total (without water)30,0232
Polymers30,0232
Non-polymers00
Water4,017223
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2940 Å2
ΔGint-23 kcal/mol
Surface area12080 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)52.923, 71.514, 70.188
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein GITR ligand / Glucocorticoid-induced-tumor necrosis factor receptor ligand


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 / water / Water


Mass: 18.015 Da / Num. of mol.: 223 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.21 Å3/Da / Density % sol: 44.36 %
Crystal growTemperature: 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

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 1.74332 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: May 1, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.74332 Å / Relative weight: 1
ReflectionRedundancy: 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
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsChi squaredRedundancy
4.55010010.0411.11712.3
3.574.599.910.0340.98412.4
3.123.5799.810.0361.0212.4
2.843.1299.310.0451.10612.3
2.632.8498.910.0551.12112.2
2.482.6398.310.0691.21712.2
2.352.4898.110.0821.2911.7
2.252.3588.110.0911.38.9
2.162.2567.310.1021.3957.5
2.092.1652.910.1211.3676
ReflectionResolution: 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
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.09-2.1660.12116111.367152.9
2.16-2.257.50.10220751.395167.3
2.25-2.358.90.09127021.3188.1
2.35-2.4811.70.08230031.29198.1
2.48-2.6312.20.06930371.217198.3
2.63-2.8412.20.05530151.121198.9
2.84-3.1212.30.04530491.106199.3
3.12-3.5712.40.03630631.02199.8
3.57-4.512.40.03430580.984199.9
4.5-5012.30.04130811.1171100

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMAC5.2.0019refinement
PDB_EXTRACT2data extraction
ADSCQuantumdata collection
HKL-2000data reduction
SHELXDphasing
SHELXEmodel building
RefinementMethod 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
RfactorNum. reflection% reflectionSelection details
Rfree0.229 750 5.1 %RANDOM
Rwork0.174 ---
all0.177 14834 --
obs0.177 14834 90.2 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 21.558 Å2
Baniso -1Baniso -2Baniso -3
1-0.81 Å20 Å20 Å2
2--0.56 Å20 Å2
3----1.37 Å2
Refinement stepCycle: LAST / Resolution: 2.09→50.06 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1982 0 0 223 2205
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0222082
X-RAY DIFFRACTIONr_angle_refined_deg1.3721.9632833
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.7085254
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.94225.81486
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.58215378
X-RAY DIFFRACTIONr_chiral_restr0.0870.2313
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.021554
X-RAY DIFFRACTIONr_nbd_refined0.1930.2848
X-RAY DIFFRACTIONr_nbtor_refined0.3060.21421
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1430.2199
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1340.234
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1520.214
X-RAY DIFFRACTIONr_mcbond_it0.8391.51310
X-RAY DIFFRACTIONr_mcangle_it1.33822072
X-RAY DIFFRACTIONr_scbond_it2.1663911
X-RAY DIFFRACTIONr_scangle_it3.3154.5761
LS refinement shellResolution: 2.09→2.139 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.202 28 -
Rwork0.182 576 -
obs-604 50.76 %

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