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- PDB-1md6: High resolution crystal structure of murine IL-1F5 reveals unique... -

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Basic information

Entry
Database: PDB / ID: 1md6
TitleHigh resolution crystal structure of murine IL-1F5 reveals unique loop conformation for specificity
Componentsinterleukin 1 family, member 5 (delta)
KeywordsIMMUNE SYSTEM / beta triple / alpha helix
Function / homology
Function and homology information


Interleukin-36 pathway / negative regulation of cytokine-mediated signaling pathway / antifungal humoral response / negative regulation of interleukin-17 production / interleukin-1 receptor binding / negative regulation of interleukin-6 production / negative regulation of type II interferon production / cytokine activity / inflammatory response / innate immune response ...Interleukin-36 pathway / negative regulation of cytokine-mediated signaling pathway / antifungal humoral response / negative regulation of interleukin-17 production / interleukin-1 receptor binding / negative regulation of interleukin-6 production / negative regulation of type II interferon production / cytokine activity / inflammatory response / innate immune response / extracellular space / cytoplasm
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-36 receptor antagonist protein
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsPei, X.Y. / Dunn, E.F. / Gay, N.J. / O'Neill, L.A.
CitationJournal: Biochemistry / Year: 2003
Title: High-Resolution Structure of Murine Interleukin 1 Homologue IL-1F5 Reveals Unique Loop Conformations for Receptor Binding Specificity.
Authors: Dunn, E.F. / Gay, N.J. / Bristow, A.F. / Gearing, D.P. / O'Neill, L.A. / Pei, X.Y.
History
DepositionAug 7, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 30, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 30, 2024Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_initial_refinement_model / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: interleukin 1 family, member 5 (delta)


Theoretical massNumber of molelcules
Total (without water)16,8881
Polymers16,8881
Non-polymers00
Water3,387188
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)78.932, 78.932, 69.740
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein interleukin 1 family, member 5 (delta) / IL-1F5 / interleukin-1F5 / interleukin 1 receptor antagonist homolog 1


Mass: 16888.305 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Plasmid: pET21a / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q9QYY1
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 188 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 3.71 Å3/Da / Density % sol: 66.86 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: ammomium sulphate, HEPES, potassium chloride, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Crystal grow
*PLUS
Temperature: 18 ℃ / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formulaDetails
15 mg/mlprotein1drop
20.1 M1reservoirKCl
30.1 MHEPES1reservoirpH7.5
41.3 Mammonium sulfate1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.934 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Feb 28, 2002 / Details: mirrors
RadiationMonochromator: Yale Mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.934 Å / Relative weight: 1
ReflectionResolution: 1.5→39.5 Å / Num. obs: 40586 / % possible obs: 100 % / Observed criterion σ(F): 1.4 / Observed criterion σ(I): 2.5 / Redundancy: 6.5 % / Biso Wilson estimate: 19.3 Å2 / Rmerge(I) obs: 0.085 / Rsym value: 0.078 / Net I/σ(I): 18.9
Reflection shellResolution: 1.5→1.58 Å / Redundancy: 7 % / Rmerge(I) obs: 0.478 / Mean I/σ(I) obs: 3.7 / Num. unique all: 39005 / Rsym value: 0.478 / % possible all: 100
Reflection
*PLUS
Highest resolution: 1.58 Å / Num. obs: 40560 / Rmerge(I) obs: 0.078
Reflection shell
*PLUS
Redundancy: 7 % / Mean I/σ(I) obs: 1.4

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALAdata scaling
AMoREphasing
CNS1refinement
CCP4(SCALA)data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2mib

2mib


Resolution: 1.6→39.5 Å / Isotropic thermal model: anisotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber / Details: maximum likelihood target using amplitudes
RfactorNum. reflection% reflectionSelection details
Rfree0.213 1684 -RANDOM
Rwork0.204 ---
all-33512 --
obs-33500 5 %-
Displacement parametersBiso mean: 23 Å2
Baniso -1Baniso -2Baniso -3
1--4.066 Å2-1.35 Å20 Å2
2---4.066 Å20 Å2
3---8.15 Å2
Refine analyzeLuzzati coordinate error obs: 0.13 Å / Luzzati d res low obs: 5 Å / Luzzati sigma a obs: 0.15 Å
Refinement stepCycle: LAST / Resolution: 1.6→39.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1185 0 0 188 1373
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_angle_d1.4
X-RAY DIFFRACTIONc_dihedral_angle_d24.7
X-RAY DIFFRACTIONc_improper_angle_d0.89
LS refinement shellResolution: 1.6→1.7 Å / Rfactor Rfree error: 0.016
RfactorNum. reflection% reflection
Rfree0.259 260 -
Rwork0.241 --
obs-5234 4.7 %
Refinement
*PLUS
Rfactor Rfree: 0.212 / Rfactor Rwork: 0.202
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg24.7
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.89

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