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- PDB-2i1b: CRYSTALLOGRAPHIC REFINEMENT OF INTERLEUKIN-1 BETA AT 2.0 ANGSTROM... -

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Entry
Database: PDB / ID: 2i1b
TitleCRYSTALLOGRAPHIC REFINEMENT OF INTERLEUKIN-1 BETA AT 2.0 ANGSTROMS RESOLUTION
ComponentsINTERLEUKIN-1 BETA
KeywordsCYTOKINE
Function / homology
Function and homology information


positive regulation of T cell mediated immunity / negative regulation of adiponectin secretion / negative regulation of lipid metabolic process / smooth muscle adaptation / negative regulation of D-glucose transmembrane transport / positive regulation of lipid catabolic process / positive regulation of cell adhesion molecule production / regulation of nitric-oxide synthase activity / positive regulation of T-helper 1 cell cytokine production / hyaluronan biosynthetic process ...positive regulation of T cell mediated immunity / negative regulation of adiponectin secretion / negative regulation of lipid metabolic process / smooth muscle adaptation / negative regulation of D-glucose transmembrane transport / positive regulation of lipid catabolic process / positive regulation of cell adhesion molecule production / regulation of nitric-oxide synthase activity / positive regulation of T-helper 1 cell cytokine production / hyaluronan biosynthetic process / positive regulation of complement activation / cellular response to interleukin-17 / positive regulation of RNA biosynthetic process / monocyte aggregation / positive regulation of tight junction disassembly / positive regulation of prostaglandin secretion / positive regulation of immature T cell proliferation in thymus / negative regulation of gap junction assembly / vascular endothelial growth factor production / positive regulation of fever generation / positive regulation of prostaglandin biosynthetic process / regulation of defense response to virus by host / positive regulation of platelet-derived growth factor receptor signaling pathway / CASP5-mediated substrate cleavage / CASP4-mediated substrate cleavage / CLEC7A/inflammasome pathway / regulation of establishment of endothelial barrier / Interleukin-1 processing / positive regulation of granulocyte macrophage colony-stimulating factor production / positive regulation of glial cell proliferation / positive regulation of monocyte chemotactic protein-1 production / positive regulation of macrophage derived foam cell differentiation / positive regulation of p38MAPK cascade / interleukin-1 receptor binding / negative regulation of synaptic transmission / positive regulation of vascular endothelial growth factor receptor signaling pathway / positive regulation of heterotypic cell-cell adhesion / positive regulation of membrane protein ectodomain proteolysis / regulation of canonical NF-kappaB signal transduction / interleukin-1-mediated signaling pathway / positive regulation of neuroinflammatory response / Interleukin-10 signaling / regulation of insulin secretion / negative regulation of extrinsic apoptotic signaling pathway in absence of ligand / Pyroptosis / positive regulation of vascular endothelial growth factor production / regulation of neurogenesis / regulation of ERK1 and ERK2 cascade / negative regulation of lipid catabolic process / positive regulation of epithelial to mesenchymal transition / embryo implantation / Purinergic signaling in leishmaniasis infection / negative regulation of MAPK cascade / positive regulation of protein export from nucleus / positive regulation of interleukin-2 production / negative regulation of insulin receptor signaling pathway / positive regulation of T cell proliferation / positive regulation of mitotic nuclear division / secretory granule / cytokine activity / response to interleukin-1 / positive regulation of interleukin-8 production / cellular response to xenobiotic stimulus / cellular response to mechanical stimulus / positive regulation of type II interferon production / positive regulation of non-canonical NF-kappaB signal transduction / positive regulation of interleukin-6 production / positive regulation of JNK cascade / negative regulation of neurogenesis / integrin binding / positive regulation of nitric oxide biosynthetic process / cytokine-mediated signaling pathway / positive regulation of angiogenesis / positive regulation of inflammatory response / Interleukin-1 signaling / cell-cell signaling / cellular response to lipopolysaccharide / response to lipopolysaccharide / Interleukin-4 and Interleukin-13 signaling / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / positive regulation of MAPK cascade / positive regulation of ERK1 and ERK2 cascade / positive regulation of canonical NF-kappaB signal transduction / lysosome / defense response to Gram-positive bacterium / inflammatory response / positive regulation of cell migration / immune response / apoptotic process / negative regulation of cell population proliferation / protein domain specific binding / positive regulation of gene expression / positive regulation of cell population proliferation / positive regulation of DNA-templated transcription / signal transduction / extracellular region / cytosol
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 / Resolution: 2 Å
AuthorsPriestle, J.P. / Schaer, H.-P. / Gruetter, M.G.
Citation
Journal: Proc.Natl.Acad.Sci.USA / Year: 1989
Title: Crystallographic refinement of interleukin 1 beta at 2.0 A resolution.
Authors: Priestle, J.P. / Schar, H.P. / Grutter, M.G.
#1: Journal: Biochem.Soc.Trans. / Year: 1988
Title: The Three-Dimensional Structure of Interleukin-1Beta
Authors: Priestle, J.P. / Schaer, H.-P. / Gruetter, M.G.
#2: Journal: Embo J. / Year: 1988
Title: Crystal Structure of the Cytokine Interleukin-1Beta
Authors: Priestle, J.P. / Schaer, H.-P. / Gruetter, M.G.
#3: Journal: J.Biol.Chem. / Year: 1987
Title: Crystallization and Preliminary X-Ray Diffraction Studies of Recombinant Human Interleukin-1Beta
Authors: Schaer, H.-P. / Priestle, J.P. / Gruetter, M.G.
History
DepositionJan 2, 1990Processing site: BNL
Revision 1.0Apr 15, 1990Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 29, 2017Group: Derived calculations / Other
Category: pdbx_database_status / struct_conf / struct_conf_type
Item: _pdbx_database_status.process_site
Revision 1.4Sep 9, 2020Group: Database references / Category: citation / Item: _citation.title
Revision 1.5Feb 21, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Remark 700SHEET THE SHEET PRESENTED AS * B1* ON SHEET RECORDS BELOW IS ACTUALLY A SIX-STRANDED BETA-BARREL. ...SHEET THE SHEET PRESENTED AS * B1* ON SHEET RECORDS BELOW IS ACTUALLY A SIX-STRANDED BETA-BARREL. THIS IS REPRESENTED BY A SEVEN-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: INTERLEUKIN-1 BETA


Theoretical massNumber of molelcules
Total (without water)17,3961
Polymers17,3961
Non-polymers00
Water3,027168
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)54.900, 54.900, 76.800
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number78
Space group name H-MP43
Atom site foot note1: POSITIONS OF ALA 1, PRO 2, AND SER 153 ARE QUESTIONABLE.
2: POSITIONS OF THE SIDE CHAINS OF GLN 34, GLU 37, GLN 48, GLU 50, GLU 51, ASN 53, ASP 54, GLU 64, ASP 75, LYS 77, LYS 88, LYS 93, LYS 94, LYS 97, AND GLU 141 ARE QUESTIONABLE.
3: RESIDUE PRO 91 IS A CIS PROLINE.

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Components

#1: Protein INTERLEUKIN-1 BETA


Mass: 17395.832 Da / Num. of mol.: 1
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.: 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: 3.33 Å3/Da / Density % sol: 63.01 %
Crystal grow
*PLUS
Method: unknown
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
17.6 mg/mlprotein11
229 %(w/v)ammonium sulfate12

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Data collection

Reflection
*PLUS
Highest resolution: 2 Å / Lowest resolution: 6.32 Å / Num. obs: 14926 / Rmerge(I) obs: 0.148

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Processing

SoftwareName: PROLSQ / Classification: refinement
RefinementResolution: 2→6 Å / Rfactor obs: 0.172
Details: AUTHORS DECLARE THAT THE POSITIONS OF ALA 1, PRO 2, AND SER 153 ARE QUESTIONABLE. ALSO THE POSITIONS OF THE SIDE CHAINS OF GLN 34, GLU 37, GLN 48, GLU 50, GLU 51, ASN 53, ASP 54, GLU 64, ASP ...Details: AUTHORS DECLARE THAT THE POSITIONS OF ALA 1, PRO 2, AND SER 153 ARE QUESTIONABLE. ALSO THE POSITIONS OF THE SIDE CHAINS OF GLN 34, GLU 37, GLN 48, GLU 50, GLU 51, ASN 53, ASP 54, GLU 64, ASP 75, LYS 77, LYS 88, LYS 93, LYS 94, LYS 97, AND GLU 141 ARE QUESTIONABLE.
Refinement stepCycle: LAST / Resolution: 2→6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1219 0 0 168 1387
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.010.02
X-RAY DIFFRACTIONp_angle_d0.0350.04
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.0330.05
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it2.9954
X-RAY DIFFRACTIONp_mcangle_it4.7816
X-RAY DIFFRACTIONp_scbond_it7.90110
X-RAY DIFFRACTIONp_scangle_it11.47615
X-RAY DIFFRACTIONp_plane_restr0.010.02
X-RAY DIFFRACTIONp_chiral_restr0.1290.15
X-RAY DIFFRACTIONp_singtor_nbd0.1930.5
X-RAY DIFFRACTIONp_multtor_nbd0.240.5
X-RAY DIFFRACTIONp_xhyhbond_nbd0.3380.5
X-RAY DIFFRACTIONp_xyhbond_nbd
X-RAY DIFFRACTIONp_planar_tor23
X-RAY DIFFRACTIONp_staggered_tor1715
X-RAY DIFFRACTIONp_orthonormal_tor13.220
X-RAY DIFFRACTIONp_transverse_tor
X-RAY DIFFRACTIONp_special_tor
Refinement
*PLUS
Highest resolution: 2 Å / Lowest resolution: 6 Å / Num. reflection all: 14331 / Rfactor all: 0.172
Solvent computation
*PLUS
Displacement parameters
*PLUS

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