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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


smooth muscle adaptation / positive regulation of T cell mediated immunity / positive regulation of myosin light chain kinase activity / negative regulation of adiponectin secretion / monocyte aggregation / negative regulation of lipid metabolic process / positive regulation of lipid catabolic process / negative regulation of D-glucose transmembrane transport / regulation of nitric-oxide synthase activity / positive regulation of cell adhesion molecule production ...smooth muscle adaptation / positive regulation of T cell mediated immunity / positive regulation of myosin light chain kinase activity / negative regulation of adiponectin secretion / monocyte aggregation / negative regulation of lipid metabolic process / positive regulation of lipid catabolic process / negative regulation of D-glucose transmembrane transport / regulation of nitric-oxide synthase activity / positive regulation of cell adhesion molecule production / hyaluronan biosynthetic process / positive regulation of T-helper 1 cell cytokine production / positive regulation of complement activation / positive regulation of calcidiol 1-monooxygenase activity / sequestering of triglyceride / cellular response to interleukin-17 / positive regulation of RNA biosynthetic process / 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 / 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 / response to carbohydrate / positive regulation of monocyte chemotactic protein-1 production / interleukin-1 receptor binding / positive regulation of vascular endothelial growth factor receptor signaling pathway / positive regulation of heterotypic cell-cell adhesion / negative regulation of synaptic transmission / positive regulation of membrane protein ectodomain proteolysis / regulation of canonical NF-kappaB signal transduction / positive regulation of granulocyte macrophage colony-stimulating factor production / interleukin-1-mediated signaling pathway / positive regulation of p38MAPK cascade / response to ATP / Interleukin-10 signaling / positive regulation of cell division / regulation of neurogenesis / negative regulation of extrinsic apoptotic signaling pathway in absence of ligand / positive regulation of vascular endothelial growth factor production / ectopic germ cell programmed cell death / Pyroptosis / negative regulation of lipid catabolic process / Purinergic signaling in leishmaniasis infection / positive regulation of epithelial to mesenchymal transition / negative regulation of MAP kinase activity / positive regulation of T cell proliferation / positive regulation of glial cell proliferation / extrinsic apoptotic signaling pathway in absence of ligand / JNK cascade / negative regulation of insulin receptor signaling pathway / neutrophil chemotaxis / embryo implantation / positive regulation of interleukin-2 production / regulation of insulin secretion / positive regulation of mitotic nuclear division / response to interleukin-1 / regulation of ERK1 and ERK2 cascade / positive regulation of protein export from nucleus / secretory granule / cytokine activity / positive regulation of interleukin-8 production / astrocyte activation / positive regulation of JNK cascade / positive regulation of DNA-binding transcription factor activity / positive regulation of MAP kinase activity / cytokine-mediated signaling pathway / negative regulation of neurogenesis / positive regulation of inflammatory response / positive regulation of interleukin-6 production / cellular response to mechanical stimulus / Interleukin-1 signaling / positive regulation of non-canonical NF-kappaB signal transduction / positive regulation of type II interferon production / positive regulation of angiogenesis / positive regulation of nitric oxide biosynthetic process / integrin binding / cellular response to xenobiotic stimulus / cell-cell signaling / positive regulation of NF-kappaB transcription factor activity / cellular response to lipopolysaccharide / Interleukin-4 and Interleukin-13 signaling / positive regulation of canonical NF-kappaB signal transduction / response to lipopolysaccharide / lysosome / defense response to Gram-positive bacterium / positive regulation of cell migration / inflammatory response / immune response / positive regulation of protein phosphorylation / negative regulation of cell population proliferation / protein domain specific binding / positive regulation of cell population proliferation / positive regulation of gene expression
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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