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- PDB-4xfu: Structure of IL-18 SER Mutant V -

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Basic information

Entry
Database: PDB / ID: 4xfu
TitleStructure of IL-18 SER Mutant V
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 / positive regulation of neuroinflammatory response / interleukin-18-mediated signaling pathway / positive regulation of interleukin-13 production / 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 / positive regulation of neuroinflammatory response / interleukin-18-mediated signaling pathway / positive regulation of interleukin-13 production / natural killer cell mediated cytotoxicity / negative regulation of myoblast differentiation / type 2 immune response / natural killer cell activation / neutrophil activation / sleep / Interleukin-1 processing / positive regulation of NK T cell proliferation / triglyceride homeostasis / positive regulation of granulocyte macrophage colony-stimulating factor production / positive regulation of natural killer cell proliferation / T-helper 1 type immune response / positive regulation of activated T cell proliferation / positive regulation of interleukin-17 production / Interleukin-10 signaling / establishment of skin barrier / Pyroptosis / regulation of cell adhesion / Purinergic signaling in leishmaniasis infection / positive regulation of chemokine production / positive regulation of tyrosine phosphorylation of STAT protein / cytokine activity / cholesterol homeostasis / 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 cold-induced thermogenesis / positive regulation of NF-kappaB transcription factor activity / Interleukin-4 and Interleukin-13 signaling / angiogenesis / cellular response to lipopolysaccharide / 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: 2.85 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_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_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


Theoretical massNumber of molelcules
Total (without water)36,3072
Polymers36,3072
Non-polymers00
Water0
1
A: Interleukin-18


Theoretical massNumber of molelcules
Total (without water)18,1541
Polymers18,1541
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Interleukin-18


Theoretical massNumber of molelcules
Total (without water)18,1541
Polymers18,1541
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area770 Å2
ΔGint-9 kcal/mol
Surface area15850 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.688, 52.032, 123.368
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 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: 18153.602 Da / Num. of mol.: 2 / Mutation: P57R, K67A, E69A, K70A, I71A, S105R
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

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 1.93 Å3/Da / Density % sol: 36.26 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / Details: 35% PEG 3350, 0.1M Tris, 0.1M Sodium Acetate / PH range: 8.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97918 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 19, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 2.85→50 Å / Num. obs: 6953 / % possible obs: 98.3 % / Redundancy: 5.7 % / Net I/σ(I): 9
Reflection shellResolution: 2.85→2.9 Å / Redundancy: 4.7 % / Mean I/σ(I) obs: 1.6 / % possible all: 99.9

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine: 1.9_1692)refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3F62

3f62


Resolution: 2.85→33.002 Å / SU ML: 0.37 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 27.24 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2868 833 12.67 %
Rwork0.2441 --
obs0.2494 6572 96.07 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.85→33.002 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2418 0 0 0 2418
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0062464
X-RAY DIFFRACTIONf_angle_d1.1193296
X-RAY DIFFRACTIONf_dihedral_angle_d17.01954
X-RAY DIFFRACTIONf_chiral_restr0.041358
X-RAY DIFFRACTIONf_plane_restr0.005430
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8501-3.02850.3831140.3126765X-RAY DIFFRACTION80
3.0285-3.26220.3221340.2932960X-RAY DIFFRACTION97
3.2622-3.59010.31191280.2591970X-RAY DIFFRACTION99
3.5901-4.10870.28741500.2422967X-RAY DIFFRACTION100
4.1087-5.17340.24711450.19731019X-RAY DIFFRACTION100
5.1734-33.00470.28091620.25141058X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: -18.1655 Å / Origin y: 0.6498 Å / Origin z: -5.151 Å
111213212223313233
T0.1988 Å2-0.0048 Å2-0.0078 Å2-0.1505 Å20.0306 Å2--0.2484 Å2
L0.9467 °20.0411 °2-0.5235 °2-0.5506 °20.1974 °2--1.9263 °2
S-0.0039 Å °0.0432 Å °0.0086 Å °0.0202 Å °0.0048 Å °-0.0318 Å °-0.1737 Å °-0.0026 Å °0.0002 Å °
Refinement TLS groupSelection details: all

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