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- PDB-1l2h: Crystal structure of Interleukin 1-beta F42W/W120F mutant -

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Basic information

Entry
Database: PDB / ID: 1l2h
TitleCrystal structure of Interleukin 1-beta F42W/W120F mutant
ComponentsInterleukin 1-beta
KeywordsIMMUNE SYSTEM / Interleukin-1 beta / beta-trefoil / F42W/W120F double mutant / protein folding / MAD phasing / hemihedral twinning
Function / homology
Function and homology information


positive regulation of T cell mediated immunity / positive regulation of cell adhesion molecule production / negative regulation of adiponectin secretion / monocyte aggregation / negative regulation of lipid metabolic process / smooth muscle adaptation / positive regulation of lipid catabolic process / negative regulation of D-glucose transmembrane transport / regulation of nitric-oxide synthase activity / hyaluronan biosynthetic process ...positive regulation of T cell mediated immunity / positive regulation of cell adhesion molecule production / negative regulation of adiponectin secretion / monocyte aggregation / negative regulation of lipid metabolic process / smooth muscle adaptation / positive regulation of lipid catabolic process / negative regulation of D-glucose transmembrane transport / regulation of nitric-oxide synthase activity / hyaluronan biosynthetic process / positive regulation of T-helper 1 cell cytokine production / positive regulation of complement activation / : / cellular response to interleukin-17 / positive regulation of RNA biosynthetic process / positive regulation of tight junction disassembly / negative regulation of gap junction assembly / positive regulation of prostaglandin biosynthetic process / positive regulation of immature T cell proliferation in thymus / vascular endothelial growth factor production / positive regulation of prostaglandin secretion / positive regulation of neuroinflammatory response / positive regulation of platelet-derived growth factor receptor signaling pathway / regulation of defense response to virus by host / fever generation / positive regulation of fever generation / regulation of establishment of endothelial barrier / CLEC7A/inflammasome pathway / Interleukin-1 processing / negative regulation of synaptic transmission / response to carbohydrate / positive regulation of monocyte chemotactic protein-1 production / interleukin-1 receptor binding / positive regulation of heterotypic cell-cell adhesion / positive regulation of macrophage derived foam cell differentiation / positive regulation of p38MAPK cascade / positive regulation of membrane protein ectodomain proteolysis / positive regulation of vascular endothelial growth factor receptor signaling pathway / positive regulation of granulocyte macrophage colony-stimulating factor production / regulation of canonical NF-kappaB signal transduction / interleukin-1-mediated signaling pathway / response to ATP / Interleukin-10 signaling / positive regulation of cell division / regulation of neurogenesis / positive regulation of vascular endothelial growth factor production / negative regulation of extrinsic apoptotic signaling pathway in absence of ligand / negative regulation of MAP kinase activity / Pyroptosis / ectopic germ cell programmed cell death / negative regulation of lipid catabolic process / regulation of ERK1 and ERK2 cascade / Purinergic signaling in leishmaniasis infection / positive regulation of epithelial to mesenchymal transition / positive regulation of T cell proliferation / extrinsic apoptotic signaling pathway in absence of ligand / JNK cascade / positive regulation of glial cell proliferation / neutrophil chemotaxis / embryo implantation / negative regulation of insulin receptor signaling pathway / positive regulation of interleukin-2 production / response to interleukin-1 / positive regulation of mitotic nuclear division / regulation of insulin secretion / secretory granule / positive regulation of protein export from nucleus / cytokine activity / positive regulation of interleukin-8 production / astrocyte activation / positive regulation of JNK cascade / positive regulation of non-canonical NF-kappaB signal transduction / cytokine-mediated signaling pathway / negative regulation of neurogenesis / positive regulation of interleukin-6 production / positive regulation of type II interferon production / Interleukin-1 signaling / cellular response to mechanical stimulus / positive regulation of inflammatory response / positive regulation of angiogenesis / positive regulation of NF-kappaB transcription factor activity / positive regulation of nitric oxide biosynthetic process / integrin binding / cellular response to xenobiotic stimulus / cell-cell signaling / cellular response to lipopolysaccharide / Interleukin-4 and Interleukin-13 signaling / response to lipopolysaccharide / positive regulation of canonical NF-kappaB signal transduction / lysosome / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / positive regulation of ERK1 and ERK2 cascade / positive regulation of MAPK cascade / defense response to Gram-positive bacterium / immune response / positive regulation of cell migration / inflammatory response / protein domain specific binding / negative regulation of cell population proliferation / apoptotic process
Similarity search - Function
Interleukin-1 propeptide / Interleukin-1 propeptide / Interleukin-1 conserved site / Interleukin-1 signature. / Interleukin-1 homologues / Interleukin-1 family / Interleukin-1 / 18 / Cytokine IL1/FGF / Trefoil (Acidic Fibroblast Growth Factor, subunit A) - #50 / Trefoil (Acidic Fibroblast Growth Factor, subunit A) ...Interleukin-1 propeptide / Interleukin-1 propeptide / Interleukin-1 conserved site / Interleukin-1 signature. / Interleukin-1 homologues / 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 / MAD / Resolution: 1.54 Å
AuthorsRudolph, M.G. / Kelker, M.S. / Schneider, T.R. / Yeates, T.O. / Oseroff, V. / Heidary, D.K. / Jennings, P.A. / Wilson, I.A.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2003
Title: Use of multiple anomalous dispersion to phase highly merohedrally twinned crystals of interleukin-1beta.
Authors: Rudolph, M.G. / Kelker, M.S. / Schneider, T.R. / Yeates, T.O. / Oseroff, V. / Heidary, D.K. / Jennings, P.A. / Wilson, I.A.
History
DepositionFeb 21, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 4, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 27, 2021Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.4Feb 14, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Interleukin 1-beta


Theoretical massNumber of molelcules
Total (without water)17,3961
Polymers17,3961
Non-polymers00
Water2,270126
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)53.890, 53.890, 77.360
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number78
Space group name H-MP43

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Components

#1: Protein Interleukin 1-beta


Mass: 17395.834 Da / Num. of mol.: 1 / Mutation: F42W, W120F
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / References: UniProt: P01584
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 126 / 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: 2.93 Å3/Da / Density % sol: 61.89 %
Crystal growTemperature: 295 K / Method: vapor diffusion
Details: ammonium sulphate, DTT, PIPES, VAPOR DIFFUSION, temperature 295K
Crystal grow
*PLUS
pH: 7 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
111.6 mg/mlprotein1drop
250 mMPIPES-NaOH1reservoirpH7.0
32.0-2.2 Mammonium sulfate1reservoir
45 mMdithiothreitol1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 1.0332 Å
DetectorType: CUSTOM-MADE / Detector: CCD / Date: Nov 22, 2000
RadiationMonochromator: Double crystal monochromator Si-111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 1.54→20 Å / Num. obs: 31800 / % possible obs: 97.1 % / Observed criterion σ(I): 0 / Redundancy: 7.6 % / Biso Wilson estimate: 22.7 Å2 / Rsym value: 0.074 / Net I/σ(I): 23.4
Reflection shellResolution: 1.54→1.6 Å / Redundancy: 5.2 % / Mean I/σ(I) obs: 2.6 / Num. unique all: 3196 / Rsym value: 0.516 / % possible all: 98.2
Reflection
*PLUS
Lowest resolution: 20 Å / Rmerge(I) obs: 0.074
Reflection shell
*PLUS
% possible obs: 98.2 % / Num. unique obs: 3196 / Rmerge(I) obs: 0.516

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
SOLVEphasing
SHELXL-97refinement
RefinementMethod to determine structure: MAD / Resolution: 1.54→18 Å / Num. parameters: 5180 / Num. restraintsaints: 4759 / Isotropic thermal model: Isotropic / Cross valid method: FREE R / σ(F): 0 / Stereochemistry target values: Engh & Huber
Details: BULK SOLVENT MODELING METHOD USED: MOEWS & KRETSINGER, J.MOL.BIOL.91(1973)201-228
RfactorNum. reflection% reflectionSelection details
Rfree0.193 1519 4.8 %RANDOM
Rwork0.154 ---
all-31781 --
obs-31781 92.7 %-
Displacement parametersBiso mean: 26.9 Å2
Refine analyzeNum. disordered residues: 3 / Occupancy sum hydrogen: 1164 / Occupancy sum non hydrogen: 1287
FreeObs
Luzzati coordinate error0.19 Å0.15 Å
Luzzati d res low-5 Å
Luzzati sigma a0.2 Å0.16 Å
Refinement stepCycle: LAST / Resolution: 1.54→18 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1168 0 0 126 1294
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.012
X-RAY DIFFRACTIONs_angle_d0.03
X-RAY DIFFRACTIONs_similar_dist0
X-RAY DIFFRACTIONs_from_restr_planes0.0347
X-RAY DIFFRACTIONs_zero_chiral_vol0.056
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.063
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.042
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.072
X-RAY DIFFRACTIONs_approx_iso_adps0
LS refinement shellResolution: 1.54→1.6 Å
RfactorNum. reflection% reflection
Rfree0.4 121 -
Rwork0.32 --
obs-2752 93.24 %
Software
*PLUS
Name: SHELXL / Version: 97 / Classification: refinement
Refinement
*PLUS
Lowest resolution: 18 Å / Num. reflection obs: 30261 / % reflection Rfree: 5 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_angle_d
X-RAY DIFFRACTIONs_angle_deg2.6
X-RAY DIFFRACTIONs_dihedral_angle_d
X-RAY DIFFRACTIONs_dihedral_angle_deg28.3

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