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- PDB-3fc0: 1.8 A crystal structure of murine GITR ligand dimer expressed in ... -

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Basic information

Entry
Database: PDB / ID: 3fc0
Title1.8 A crystal structure of murine GITR ligand dimer expressed in Drosophila melanogaster S2 cells
ComponentsGITR ligand
KeywordsPROTEIN 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
Tumor necrosis factor ligand superfamily member 18 / TNF(Tumour Necrosis Factor) family / Tumour necrosis factor domain / Tumor necrosis factor (TNF) homology domain (THD) profile. / Jelly Rolls - #40 / Tumour necrosis factor-like domain superfamily / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
ACETATE ION / Tumor necrosis factor ligand superfamily member 18
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.76 Å
AuthorsChattopadhyay, K. / Ramagopal, U.A. / Nathenson, S.G. / Almo, S.C.
CitationJournal: 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
DepositionNov 20, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 30, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software
Revision 1.3Sep 6, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: GITR ligand
B: GITR ligand
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,8643
Polymers31,8052
Non-polymers591
Water1,65792
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3230 Å2
ΔGint-26 kcal/mol
Surface area11400 Å2
MethodPISA
Unit cell
Length a, b, c (Å)52.609, 69.293, 73.994
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein GITR ligand / Glucocorticoid-induced-tumor necrosis factor receptor ligand / Tumor necrosis factor (Ligand) ...Glucocorticoid-induced-tumor necrosis factor receptor ligand / Tumor necrosis factor (Ligand) superfamily / member 18


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 / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 92 / 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: 2.12 Å3/Da / Density % sol: 41.99 %
Crystal growTemperature: 298 K / pH: 7
Details: 15% Tacsimate pH 7.0, 0.1M Hepes, 2% PEG 3350, Vapor diffusion, Sitting drop, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 0.979
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 14, 2008
RadiationProtocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 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 shellResolution: 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

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACT3.006data extraction
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2QDN

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
RfactorNum. reflection% reflectionSelection details
Rfree0.262 1357 5 %RANDOM
Rwork0.224 ---
obs0.226 27086 98.5 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 30.95 Å2
Baniso -1Baniso -2Baniso -3
1--0.38 Å20 Å20 Å2
2---3 Å20 Å2
3---3.38 Å2
Refinement stepCycle: LAST / Resolution: 1.76→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1932 0 4 92 2028
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0221988
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.5441.962699
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.0525239
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.20325.44379
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.15615347
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.1170.2304
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0211458
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.041.51211
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.87921976
X-RAY DIFFRACTIONr_scbond_it2.7853777
X-RAY DIFFRACTIONr_scangle_it4.4944.5723
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.76→1.8 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.286 81 -
Rwork0.254 1578 -
obs--82.87 %

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