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- PDB-1ilt: X-RAY STRUCTURE OF INTERLEUKIN-1 RECEPTOR ANTAGONIST AT 2.0 ANGST... -

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Basic information

Entry
Database: PDB / ID: 1ilt
TitleX-RAY STRUCTURE OF INTERLEUKIN-1 RECEPTOR ANTAGONIST AT 2.0 ANGSTROMS RESOLUTION
ComponentsINTERLEUKIN-1 RECEPTOR ANTAGONIST
KeywordsCYTOKINE
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
Similarity search - Domain/homology
Interleukin-1 receptor antagonist protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / Resolution: 2 Å
AuthorsBrandhuber, B.J. / Vigers, G.P.A.
CitationJournal: J.Biol.Chem. / Year: 1994
Title: X-ray structure of interleukin-1 receptor antagonist at 2.0-A resolution.
Authors: Vigers, G.P. / Caffes, P. / Evans, R.J. / Thompson, R.C. / Eisenberg, S.P. / Brandhuber, B.J.
History
DepositionMar 9, 1994Processing site: BNL
Revision 1.0Apr 1, 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
Revision 1.4Feb 7, 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 SHEETS PRESENTED AS A1 AND B1 ON SHEET RECORDS BELOW ARE ACTUALLY A SIX-STRANDED BETA- ...SHEET THE SHEETS PRESENTED AS A1 AND B1 ON SHEET RECORDS BELOW ARE 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 RECEPTOR ANTAGONIST
B: INTERLEUKIN-1 RECEPTOR ANTAGONIST


Theoretical massNumber of molelcules
Total (without water)34,2912
Polymers34,2912
Non-polymers00
Water00
1
A: INTERLEUKIN-1 RECEPTOR ANTAGONIST


Theoretical massNumber of molelcules
Total (without water)17,1451
Polymers17,1451
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: INTERLEUKIN-1 RECEPTOR ANTAGONIST


Theoretical massNumber of molelcules
Total (without water)17,1451
Polymers17,1451
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)71.110, 71.110, 112.610
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 A 53 / 2: CIS PROLINE - PRO B 53
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.530352, 0.829762, 0.173845), (-0.697784, -0.310782, -0.645378), (-0.481482, -0.463584, 0.743818)
Vector: 11.1712, 93.6653, 78.1377)
DetailsTWO INDEPENDENT MOLECULES PER UNIT CELL. THE TRANSFORMATION PRESENTED ON *MTRIX* RECORDS BELOW WILL YIELD APPROXIMATE COORDINATES FOR CHAIN *B* WHEN APPLIED TO CHAIN *A*.

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Components

#1: Protein INTERLEUKIN-1 RECEPTOR ANTAGONIST / Coordinate model: Cα atoms only


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

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.07 Å3/Da / Density % sol: 40.72 %
Crystal grow
*PLUS
Temperature: 20 ℃ / pH: 6 / Method: vapor diffusion, hanging drop
Details: drop contained 1:1 mixture of precipitant and recombinant IL-lra
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
121 mg/mlIL-lra1drop
210 mMMOPS1drop
330 %PEG80001reservoirprecipitant
40.6 M1reservoirprecipitantNaCl
550 mMMES1reservoirprecipitant

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Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
Reflection
*PLUS
Highest resolution: 2 Å / Lowest resolution: 8 Å / % possible obs: 95.6 % / Rmerge(I) obs: 0.069

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Processing

Software
NameClassification
X-PLORmodel building
X-PLORrefinement
X-PLORphasing
RefinementResolution: 2→8 Å / σ(F): 2 /
RfactorNum. reflection
Rwork0.236 -
obs0.236 19076
Refinement stepCycle: LAST / Resolution: 2→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms286 0 0 0 286
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.011
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_deg
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
Refinement
*PLUS
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Type: x_angle_deg / Dev ideal: 1.9

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