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- PDB-4g4f: Crystal structure of GITRL from Bushbaby -

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Basic information

Entry
Database: PDB / ID: 4g4f
TitleCrystal structure of GITRL from Bushbaby
ComponentsTumor necrosis factor ligand superfamily member 18
KeywordsIMMUNE SYSTEM / 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 / T cell proliferation involved in immune response / regulation of T cell proliferation / tumor necrosis factor-mediated signaling pathway / cell surface
Similarity search - Function
Tumor necrosis factor ligand superfamily member 18 / Jelly Rolls - #40 / Tumour necrosis factor domain / Tumor necrosis factor (TNF) homology domain (THD) profile. / 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 speciesOtolemur garnettii (small-eared galago)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.847 Å
AuthorsKumar, P.R. / Bhosle, R. / Nathenson, S.G. / Almo, S.C. / New York Structural Genomics Research Consortium (NYSGRC) / Atoms-to-Animals: The Immune Function Network (IFN)
CitationJournal: to be published
Title: Crystal structure of GITRL from Otolemur garnettii
Authors: Kumar, P.R. / Nathenson, S.G. / Almo, S.C. / New York Structural Genomics Research Consortium (NYSGRC) / Atoms-to-Animals: The Immune Function Network (IFN)
History
DepositionJul 16, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 1, 2012Provider: repository / Type: Initial release
Revision 1.1Sep 13, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Tumor necrosis factor ligand superfamily member 18


Theoretical massNumber of molelcules
Total (without water)14,0341
Polymers14,0341
Non-polymers00
Water1,31573
1
A: Tumor necrosis factor ligand superfamily member 18

A: Tumor necrosis factor ligand superfamily member 18

A: Tumor necrosis factor ligand superfamily member 18


Theoretical massNumber of molelcules
Total (without water)42,1023
Polymers42,1023
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_455-y-1,x-y,z1
crystal symmetry operation3_445-x+y-1,-x-1,z1
Buried area3900 Å2
ΔGint-24 kcal/mol
Surface area15350 Å2
MethodPISA
2
A: Tumor necrosis factor ligand superfamily member 18
x 6


Theoretical massNumber of molelcules
Total (without water)84,2056
Polymers84,2056
Non-polymers00
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_455-y-1,x-y,z1
crystal symmetry operation3_445-x+y-1,-x-1,z1
crystal symmetry operation10_444-y-1,-x-1,-z-1/21
crystal symmetry operation11_454-x+y-1,y,-z-1/21
crystal symmetry operation12_554x,x-y,-z-1/21
Buried area9180 Å2
ΔGint-59 kcal/mol
Surface area29340 Å2
MethodPISA
Unit cell
Length a, b, c (Å)52.194, 52.194, 144.720
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number182
Space group name H-MP6322
Components on special symmetry positions
IDModelComponents
11A-231-

HOH

21A-264-

HOH

DetailsThe biological assembly is a trimer generated from the monomer in the asymmetric unit by crystallographic symmetry operations

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Components

#1: Protein Tumor necrosis factor ligand superfamily member 18


Mass: 14034.092 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Otolemur garnettii (small-eared galago)
Gene: GITRL / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: J3QW36*PLUS
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 73 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.03 Å3/Da / Density % sol: 39.33 %
Crystal growTemperature: 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-HCl pH 5.5, 0.2M Sodium Chloride, 25%(w/v) PEG3350), Cryoprotection (Reservoir + 20% MPD), temperature 298K, ...Details: Protein (20 mM Hepes, pH 7.5, 150 mM NaCl, 10% glycerol, Reservoir (0.1M Bis-Tris-HCl pH 5.5, 0.2M Sodium Chloride, 25%(w/v) PEG3350), Cryoprotection (Reservoir + 20% MPD), temperature 298K, VAPOR DIFFUSION, SITTING DROP

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.075 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 14, 2012 / Details: MIRRORS
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.075 Å / Relative weight: 1
ReflectionResolution: 1.85→50 Å / Num. obs: 10736 / % possible obs: 99.6 % / Redundancy: 7.3 % / Rmerge(I) obs: 0.088 / Net I/σ(I): 7.9
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsDiffraction-ID% possible all
1.85-1.884.50.731198.3
1.88-1.925.30.618198.8
1.92-1.956.30.4811100
1.95-1.997.60.4251100
1.99-2.047.70.341100
2.04-2.087.70.311199.8
2.08-2.147.80.2621100
2.14-2.197.60.2511100
2.19-2.267.80.2041100
2.26-2.337.80.1951100
2.33-2.417.70.168199.8
2.41-2.517.70.1521100
2.51-2.637.70.1291100
2.63-2.767.70.115199.8
2.76-2.947.60.097199.6
2.94-3.167.60.0791100
3.16-3.487.30.074199.8
3.48-3.997.40.0641100
3.99-5.027.30.052199.5
5.02-506.80.049197.9

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Processing

Software
NameVersionClassificationNB
SCALEPACKdata scaling
PHENIX1.8_1069refinement
PDB_EXTRACT3.11data extraction
CBASSdata collection
HKL-2000data reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2Q1M

2q1m


Resolution: 1.847→43.146 Å / Occupancy max: 1 / Occupancy min: 0.5 / SU ML: 0.24 / σ(F): 1.34 / Phase error: 27.02 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2438 514 4.8 %
Rwork0.2074 --
obs0.209 10699 99.58 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 43.6143 Å2
Refinement stepCycle: LAST / Resolution: 1.847→43.146 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms905 0 0 73 978
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.007936
X-RAY DIFFRACTIONf_angle_d1.1211269
X-RAY DIFFRACTIONf_dihedral_angle_d14.453343
X-RAY DIFFRACTIONf_chiral_restr0.084145
X-RAY DIFFRACTIONf_plane_restr0.004159
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8471-2.0330.30951200.24292449X-RAY DIFFRACTION99
2.033-2.32710.2981400.21642469X-RAY DIFFRACTION100
2.3271-2.93180.24681380.222528X-RAY DIFFRACTION100
2.9318-43.15750.2091160.19382739X-RAY DIFFRACTION100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
13.91840.77350.32059.0945-5.26276.5613-0.1171-0.16810.39250.480.01880.303-0.3072-0.17090.01430.31810.04180.00220.2466-0.0380.3685-13.54-3.1185-9.8091
24.14990.52840.6942.2601-0.29592.34270.0145-0.02560.15210.1613-0.0215-0.2406-0.0820.26810.06670.2213-0.00460.02370.2301-0.02170.2849-12.0328-9.8625-13.741
34.3694-4.05624.68824.8396-4.54546.64560.34680.4115-0.177-0.4514-0.2160.13090.42890.2318-0.17970.275-0.01330.01040.2769-0.05280.323-16.0452-11.5652-24.9679
44.6343-0.74530.88354.23390.16853.5491-0.08540.51840.3879-0.5044-0.0926-0.3061-0.28580.21020.08680.2336-0.0539-0.01020.26780.04320.2735-13.0415-5.4672-20.5477
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 4 through 23 )
2X-RAY DIFFRACTION2chain 'A' and (resid 24 through 60 )
3X-RAY DIFFRACTION3chain 'A' and (resid 61 through 91 )
4X-RAY DIFFRACTION4chain 'A' and (resid 92 through 121 )

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