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- PDB-1ilr: CRYSTAL STRUCTURE OF THE INTERLEUKIN-1 RECEPTOR ANTAGONIST -

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Basic information

Entry
Database: PDB / ID: 1ilr
TitleCRYSTAL STRUCTURE OF THE INTERLEUKIN-1 RECEPTOR ANTAGONIST
ComponentsINTERLEUKIN-1 RECEPTOR ANTAGONIST PROTEIN
KeywordsBINDING PROTEIN
Function / homology
Function and homology information


interleukin-1 type I receptor antagonist activity / interleukin-1 type II receptor antagonist activity / interleukin-1, type I receptor binding / interleukin-1 receptor antagonist activity / interleukin-1, type II receptor binding / negative regulation of interleukin-1-mediated signaling pathway / negative regulation of heterotypic cell-cell adhesion / interleukin-1 receptor binding / inflammatory response to antigenic stimulus / insulin secretion ...interleukin-1 type I receptor antagonist activity / interleukin-1 type II receptor antagonist activity / interleukin-1, type I receptor binding / interleukin-1 receptor antagonist activity / interleukin-1, type II receptor binding / negative regulation of interleukin-1-mediated signaling pathway / negative regulation of heterotypic cell-cell adhesion / interleukin-1 receptor binding / inflammatory response to antigenic stimulus / insulin secretion / Interleukin-10 signaling / response to glucocorticoid / cytokine activity / acute-phase response / lipid metabolic process / Interleukin-1 signaling / immune response / centrosome / extracellular space / extracellular exosome / nucleoplasm / plasma membrane / cytosol
Similarity search - Function
Interleukin-1 receptor antagonist/Interleukin-36 / 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
Interleukin-1 receptor antagonist protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / Resolution: 2.1 Å
AuthorsSchreuder, H.A. / Rondeau, J.-M. / Tardif, C.
CitationJournal: Eur.J.Biochem. / Year: 1995
Title: Refined crystal structure of the interleukin-1 receptor antagonist. Presence of a disulfide link and a cis-proline.
Authors: Schreuder, H.A. / Rondeau, J.M. / Tardif, C. / Soffientini, A. / Sarubbi, E. / Akeson, A. / Bowlin, T.L. / Yanofsky, S. / Barrett, R.W.
History
DepositionJun 20, 1994Processing site: BNL
Revision 1.0Feb 7, 1995Provider: 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
1: INTERLEUKIN-1 RECEPTOR ANTAGONIST PROTEIN
2: INTERLEUKIN-1 RECEPTOR ANTAGONIST PROTEIN


Theoretical massNumber of molelcules
Total (without water)34,2912
Polymers34,2912
Non-polymers00
Water2,504139
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)71.300, 71.300, 117.300
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
Atom site foot note1: CIS PROLINE - PRO 1 53 / 2: CIS PROLINE - PRO 2 53
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (0.342973, 0.714236, -0.61011), (-0.829805, 0.534758, 0.15955), (0.440219, 0.451551, 0.776085)
Vector: 13.4539, 50.85968, -7.88375)

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Components

#1: Protein INTERLEUKIN-1 RECEPTOR ANTAGONIST PROTEIN


Mass: 17145.406 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / References: UniProt: P18510
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 139 / 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: 2.17 Å3/Da / Density % sol: 43.39 %
Crystal grow
*PLUS
Temperature: 4 ℃ / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
15 %PEG80001drop
2100 mMTris-HCl1drop
3100 mMammonium acetate1drop
420 mg/mlIL-1ra1drop
530 mM1dropNaCl
610 mMsodium phosphate1drop
730 %PEG80001reservoir

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Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
Reflection
*PLUS
Highest resolution: 2.1 Å / Num. obs: 16972 / % possible obs: 92.7 %
Reflection shell
*PLUS
Highest resolution: 2.1 Å / Lowest resolution: 2.2 Å / % possible obs: 60.1 %

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Processing

Software
NameClassification
X-PLORmodel building
X-PLORrefinement
X-PLORphasing
RefinementResolution: 2.1→8 Å / σ(F): 0 /
RfactorNum. reflection
Rwork0.197 -
obs0.197 15610
Refinement stepCycle: LAST / Resolution: 2.1→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2285 0 0 139 2424
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.008
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.5
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Software
*PLUS
Name: X-PLOR / Classification: refinement
Refinement
*PLUS
Rfactor obs: 0.197 / Rfactor Rwork: 0.197
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Type: x_angle_d / Dev ideal: 1.5

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