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- PDB-4xft: Structure of IL-18 SER Mutant III -

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Basic information

Entry
Database: PDB / ID: 4xft
TitleStructure of IL-18 SER Mutant III
ComponentsInterleukin-18Interleukin 18
KeywordsCYTOKINE / Interleukin-18 / IL-18 / Surface Entropy Reduction / immune defense
Function / homology
Function and homology information


interleukin-18 receptor binding / Interleukin-18 signaling / positive regulation of tissue remodeling / positive regulation of T-helper 2 cell differentiation / positive regulation of T-helper 1 cell cytokine production / positive regulation of macrophage derived foam cell differentiation / neutrophil activation / positive regulation of neuroinflammatory response / interleukin-18-mediated signaling pathway / natural killer cell mediated cytotoxicity ...interleukin-18 receptor binding / Interleukin-18 signaling / positive regulation of tissue remodeling / positive regulation of T-helper 2 cell differentiation / positive regulation of T-helper 1 cell cytokine production / positive regulation of macrophage derived foam cell differentiation / neutrophil activation / positive regulation of neuroinflammatory response / interleukin-18-mediated signaling pathway / natural killer cell mediated cytotoxicity / triglyceride homeostasis / negative regulation of myoblast differentiation / type 2 immune response / natural killer cell activation / sleep / Interleukin-1 processing / positive regulation of NK T cell proliferation / positive regulation of granulocyte macrophage colony-stimulating factor production / positive regulation of interleukin-13 production / T-helper 1 type immune response / positive regulation of activated T cell proliferation / positive regulation of interleukin-17 production / Interleukin-10 signaling / positive regulation of natural killer cell proliferation / establishment of skin barrier / Pyroptosis / Purinergic signaling in leishmaniasis infection / regulation of cell adhesion / positive regulation of chemokine production / positive regulation of tyrosine phosphorylation of STAT protein / cholesterol homeostasis / cytokine activity / positive regulation of smooth muscle cell proliferation / positive regulation of inflammatory response / positive regulation of non-canonical NF-kappaB signal transduction / positive regulation of type II interferon production / cell-cell signaling / positive regulation of NF-kappaB transcription factor activity / positive regulation of cold-induced thermogenesis / angiogenesis / Interleukin-4 and Interleukin-13 signaling / cell population proliferation / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / defense response to Gram-positive bacterium / inflammatory response / positive regulation of transcription by RNA polymerase II / extracellular space / extracellular region / cytosol
Similarity search - Function
Interleukin-18 / Interleukin-1 family / Interleukin-1 / 18 / Cytokine IL1/FGF / Trefoil (Acidic Fibroblast Growth Factor, subunit A) - #50 / Trefoil (Acidic Fibroblast Growth Factor, subunit A) / Trefoil / Mainly Beta
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsKrumm, B.E. / Meng, X. / Xiang, Y. / Deng, J.
Funding support United States, 3items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI113539 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI079217 United States
Oklahoma State UniversityOKL02848 United States
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2015
Title: Crystallization of interleukin-18 for structure-based inhibitor design.
Authors: Krumm, B. / Meng, X. / Xiang, Y. / Deng, J.
History
DepositionDec 29, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 10, 2015Provider: repository / Type: Initial release
Revision 1.1Jul 1, 2015Group: Database references
Revision 1.2Sep 20, 2017Group: Advisory / Author supporting evidence ...Advisory / Author supporting evidence / Derived calculations / Source and taxonomy
Category: entity_src_gen / pdbx_audit_support ...entity_src_gen / pdbx_audit_support / pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / pdbx_struct_oper_list / pdbx_unobs_or_zero_occ_atoms
Item: _entity_src_gen.pdbx_alt_source_flag / _pdbx_audit_support.funding_organization ..._entity_src_gen.pdbx_alt_source_flag / _pdbx_audit_support.funding_organization / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_assembly_prop.type / _pdbx_struct_assembly_prop.value / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Dec 11, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Sep 27, 2023Group: Advisory / Data collection ...Advisory / 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 / pdbx_unobs_or_zero_occ_atoms
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Interleukin-18
B: Interleukin-18
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,2034
Polymers36,0472
Non-polymers1562
Water3,027168
1
A: Interleukin-18


Theoretical massNumber of molelcules
Total (without water)18,0231
Polymers18,0231
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Interleukin-18
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,1803
Polymers18,0231
Non-polymers1562
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1530 Å2
ΔGint-2 kcal/mol
Surface area15730 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.514, 55.042, 113.003
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1010A1 - 156
2010B1 - 156

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Components

#1: Protein Interleukin-18 / Interleukin 18 / IL-18 / Iboctadekin / Interferon gamma-inducing factor / IFN-gamma-inducing factor / Interleukin-1 ...IL-18 / Iboctadekin / Interferon gamma-inducing factor / IFN-gamma-inducing factor / Interleukin-1 gamma / IL-1 gamma


Mass: 18023.406 Da / Num. of mol.: 2 / Mutation: K67A, E69A, K70A, I71A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: IL18, IGIF, IL1F4 / Plasmid: pET / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) / References: UniProt: Q14116
#2: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE / Dimethyl sulfoxide


Mass: 78.133 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 168 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.35 Å3/Da / Density % sol: 47.7 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: 35% PEG 3350, 0.1M MES, 5% DMSO

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0,.97929
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 10, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
101
20.979291
ReflectionResolution: 2→50 Å / Num. obs: 24057 / % possible obs: 100 % / Redundancy: 7.2 % / Rsym value: 0.075 / Net I/σ(I): 30
Reflection shellResolution: 2→2.03 Å / Redundancy: 6.9 % / Rmerge(I) obs: 0.562 / Mean I/σ(I) obs: 3.2 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0049refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3F62

3f62


Resolution: 2→50 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.945 / SU B: 6.236 / SU ML: 0.092 / Cross valid method: THROUGHOUT / ESU R: 0.164 / ESU R Free: 0.149 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21802 1219 5.1 %RANDOM
Rwork0.17695 ---
obs0.17899 22784 99.13 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 41.6 Å2
Baniso -1Baniso -2Baniso -3
1-2.72 Å20 Å20 Å2
2---1.77 Å20 Å2
3----0.94 Å2
Refinement stepCycle: 1 / Resolution: 2→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2467 0 8 168 2643
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.022461
X-RAY DIFFRACTIONr_bond_other_d0.0030.022295
X-RAY DIFFRACTIONr_angle_refined_deg1.2951.9693318
X-RAY DIFFRACTIONr_angle_other_deg0.873.0015291
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9135314
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.63325.487113
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.38915436
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.8391510
X-RAY DIFFRACTIONr_chiral_restr0.080.2372
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0212798
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02538
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_it1.6022.9011244
X-RAY DIFFRACTIONr_mcbond_other1.6022.91243
X-RAY DIFFRACTIONr_mcangle_it2.4434.3341550
X-RAY DIFFRACTIONr_mcangle_other2.4434.3351551
X-RAY DIFFRACTIONr_scbond_it2.0743.1771217
X-RAY DIFFRACTIONr_scbond_other2.0733.1811218
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.2814.6611765
X-RAY DIFFRACTIONr_long_range_B_refined6.88523.8622672
X-RAY DIFFRACTIONr_long_range_B_other6.88323.8822673
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Number: 8422 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.1 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 1.985→2.036 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.234 77 -
Rwork0.214 1496 -
obs--89.58 %
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)
13.0424-0.04441.23011.08570.19362.9389-0.0108-0.0087-0.0368-0.2162-0.08920.09410.1302-0.29630.10.0956-0.0308-0.03110.08370.02450.056950.536778.9003123.7797
27.8195-2.2782-2.5190.80960.54991.9966-0.0440.0804-0.12780.09630.04580.2003-0.149-0.6194-0.00180.3034-0.0346-0.03930.3460.040.272240.996376.4366116.1788
34.90811.23630.24262.65050.36782.27020.1257-0.0289-0.0795-0.1834-0.09590.03960.2508-0.1913-0.02980.0589-0.0176-0.01470.04350.02320.022855.168177.2278128.1138
42.56190.450.05162.01640.00113.73630.02410.087-0.186-0.2236-0.0253-0.19850.23440.10040.00120.05250.00560.00260.01440.00010.056761.223378.7086125.2293
54.766-0.83050.28112.9402-0.06292.2822-0.03090.50810.0339-0.32760.1293-0.24260.11540.0934-0.09840.217-0.0296-0.03260.12730.00060.086156.54177.9825112.7227
64.1135-0.4650.96371.1371-0.19842.301-0.04580.14650.0723-0.04320.0190.2336-0.0307-0.22360.02670.05310.0016-0.03810.07620.02350.077436.070273.5223142.9924
73.3265-0.52951.28792.1372-0.50173.3356-0.01180.26140.1633-0.102-0.03550.2711-0.0092-0.18770.04740.0215-0.0025-0.00360.05090.00840.060639.657474.4632143.9007
84.33780.4646-0.23772.3631-0.06172.79240.0129-0.21640.19250.1994-0.02350.1884-0.1209-0.10190.01060.04010.0133-0.00770.0243-0.01920.048141.846173.3246152.3633
93.46640.59621.20631.13380.99351.0426-0.1578-0.55730.08480.25590.08640.07910.1123-0.12630.07140.21850.1290.03410.28140.02020.251226.601579.1138153.278
105.6239-0.7461-3.03343.23782.34857.3988-0.14420.0876-0.1488-0.07080.01150.19370.2127-0.28490.13270.0499-0.01-0.02630.08440.03990.155130.206867.7642147.8733
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 27
2X-RAY DIFFRACTION2A28 - 40
3X-RAY DIFFRACTION3A41 - 80
4X-RAY DIFFRACTION4A81 - 125
5X-RAY DIFFRACTION5A126 - 155
6X-RAY DIFFRACTION6B1 - 30
7X-RAY DIFFRACTION7B31 - 82
8X-RAY DIFFRACTION8B83 - 126
9X-RAY DIFFRACTION9B127 - 145
10X-RAY DIFFRACTION10B146 - 156

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