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- PDB-4db5: Crystal structure of Rabbit GITRL -

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Basic information

Entry
Database: PDB / ID: 4db5
TitleCrystal structure of Rabbit GITRL
ComponentsTumor necrosis factor ligand superfamily member 18
KeywordsIMMUNE 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 / regulation of T cell proliferation / T cell proliferation involved in immune response / tumor necrosis factor-mediated signaling pathway / positive regulation of cell adhesion / cell surface / identical protein binding / membrane
Similarity search - Function
Tumor necrosis factor ligand superfamily member 18 / Jelly Rolls - #40 / Tumour necrosis factor-like domain superfamily / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
TNF superfamily member 18
Similarity search - Component
Biological speciesOryctolagus cuniculus (rabbit)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.522 Å
AuthorsKumar, 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)
CitationJournal: 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
DepositionJan 13, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 21, 2012Provider: repository / Type: Initial release
Revision 1.1Jun 6, 2012Group: Structure summary
Revision 1.2Sep 13, 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_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Nov 20, 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,3372
Polymers14,0551
Non-polymers2821
Water2,198122
1
A: Tumor necrosis factor ligand superfamily member 18
hetero molecules

A: Tumor necrosis factor ligand superfamily member 18
hetero molecules

A: Tumor necrosis factor ligand superfamily member 18
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,0126
Polymers42,1653
Non-polymers8473
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555-z,-x,y1
crystal symmetry operation10_555-y,z,-x1
Buried area4110 Å2
ΔGint-23 kcal/mol
Surface area16900 Å2
MethodPISA
2
A: Tumor necrosis factor ligand superfamily member 18
hetero molecules
x 12


Theoretical massNumber of molelcules
Total (without water)172,04924
Polymers168,66112
Non-polymers3,38812
Water21612
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555-z,-x,y1
crystal symmetry operation10_555-y,z,-x1
crystal symmetry operation16_544x,-y-1/2,-z-1/21
crystal symmetry operation20_544-z,x-1/2,-y-1/21
crystal symmetry operation24_544-y,-z-1/2,x-1/21
crystal symmetry operation27_554-x+1/2,y,-z-1/21
crystal symmetry operation30_554z+1/2,-x,-y-1/21
crystal symmetry operation33_554y+1/2,z,x-1/21
crystal symmetry operation38_545-x+1/2,-y-1/2,z1
crystal symmetry operation41_545z+1/2,x-1/2,y1
crystal symmetry operation47_545y+1/2,-z-1/2,-x1
Buried area31390 Å2
ΔGint-152 kcal/mol
Surface area52660 Å2
MethodPISA
Unit cell
Length a, b, c (Å)127.047, 127.047, 127.047
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number196
Space group name H-MF23
Components on special symmetry positions
IDModelComponents
11A-303-

HOH

21A-404-

HOH

31A-405-

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: 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
#2: Chemical ChemComp-B3P / 2-[3-(2-HYDROXY-1,1-DIHYDROXYMETHYL-ETHYLAMINO)-PROPYLAMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL


Mass: 282.334 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H26N2O6 / Comment: pH buffer*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 122 / 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: 3.04 Å3/Da / Density % sol: 59.53 %
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 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

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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: Sep 27, 2011 / 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: 1.52→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
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.52-1.5532.80.68813010.9861100
1.55-1.57330.61212780.9581100
1.57-1.632.80.4913290.9711100
1.6-1.64330.43612860.9751100
1.64-1.6733.10.36412910.9981100
1.67-1.7133.20.33612961.0161100
1.71-1.7533.30.26412961.0381100
1.75-1.833.20.20712951.0721100
1.8-1.8633.40.16812931.0671100
1.86-1.9233.30.14213101.1251100
1.92-1.9833.30.10412971.1011100
1.98-2.0633.40.08212891.0761100
2.06-2.1633.40.06813331.0641100
2.16-2.2733.30.05912761.0481100
2.27-2.4133.50.051132311100
2.41-2.633.40.05212961.1591100
2.6-2.86330.05113281.4371100
2.86-3.2732.80.04213071.2711100
3.27-4.1331.90.02713370.8181100
4.13-5032.10.02513670.69199.3

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Processing

Software
NameVersionClassificationNB
SCALEPACKdata scaling
PHENIX1.7.3_928refinement
PDB_EXTRACT3.1data extraction
CBASSdata collection
HKL-2000data reduction
HKL-2000data scaling
PHENIX1.7.3_928phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 3FC0

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
RfactorNum. reflection% reflectionSelection details
Rfree0.1757 1333 5.1 %RANDOM
Rwork0.1606 ---
obs0.1614 26128 99.98 %-
Solvent computationShrinkage 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 parametersBiso max: 57.92 Å2 / Biso mean: 16.9381 Å2 / Biso min: 7.42 Å2
Baniso -1Baniso -2Baniso -3
1--0 Å20 Å20 Å2
2--0 Å2-0 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 1.522→29.147 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms961 0 19 122 1102
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0071101
X-RAY DIFFRACTIONf_angle_d1.1711508
X-RAY DIFFRACTIONf_chiral_restr0.08160
X-RAY DIFFRACTIONf_plane_restr0.005197
X-RAY DIFFRACTIONf_dihedral_angle_d18.525424
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 10 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
1.5217-1.5760.25161440.191624772621
1.576-1.63910.18481240.173124612585
1.6391-1.71370.19741240.16724652589
1.7137-1.80410.17211570.162124242581
1.8041-1.91710.1861330.158424822615
1.9171-2.06510.16911180.154924522570
2.0651-2.27280.18171290.147624802609
2.2728-2.60150.1831390.159424802619
2.6015-3.27690.16021460.169124892635
3.2769-29.15190.16571190.156525852704
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)
12.9317-0.3997-0.31541.75490.42993.54040.0895-0.03620.19240.0648-0.02510.4175-0.2407-0.2396-0.03670.0770.00080.05720.11210.0070.1559-2.9821-22.5775-11.6534
20.3186-0.05020.11612.13040.17280.62060.02710.02150.01980.01780.02630.02040.0389-0.0191-0.04860.07380.01670.00260.0741-0.00710.09027.2813-26.2788-21.6007
30.9396-1.44590.08484.08020.09050.67210.05940.03040.0071-0.1803-0.00980.0859-0.0468-0.0444-0.05460.04580.00350.0280.0894-0.00380.10764.1322-21.8708-20.6955
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resseq 5:26)A5 - 26
2X-RAY DIFFRACTION2chain 'A' and (resseq 27:90)A27 - 90
3X-RAY DIFFRACTION3chain 'A' and (resseq 91:125)A91 - 125

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