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- PDB-1icw: INTERLEUKIN-8, MUTANT WITH GLU 38 REPLACED BY CYS AND CYS 50 REPL... -

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Basic information

Entry
Database: PDB / ID: 1icw
TitleINTERLEUKIN-8, MUTANT WITH GLU 38 REPLACED BY CYS AND CYS 50 REPLACED BY ALA
ComponentsINTERLEUKIN-8
KeywordsCYTOKINE / CHEMOKINE
Function / homology
Function and homology information


regulation of single stranded viral RNA replication via double stranded DNA intermediate / regulation of entry of bacterium into host cell / interleukin-8 receptor binding / negative regulation of cell adhesion molecule production / CXCR chemokine receptor binding / ATF4 activates genes in response to endoplasmic reticulum stress / embryonic digestive tract development / neutrophil activation / induction of positive chemotaxis / chemokine activity ...regulation of single stranded viral RNA replication via double stranded DNA intermediate / regulation of entry of bacterium into host cell / interleukin-8 receptor binding / negative regulation of cell adhesion molecule production / CXCR chemokine receptor binding / ATF4 activates genes in response to endoplasmic reticulum stress / embryonic digestive tract development / neutrophil activation / induction of positive chemotaxis / chemokine activity / positive regulation of neutrophil chemotaxis / Chemokine receptors bind chemokines / negative regulation of G protein-coupled receptor signaling pathway / Interleukin-10 signaling / cellular response to interleukin-1 / regulation of cell adhesion / cellular response to fibroblast growth factor stimulus / neutrophil chemotaxis / response to endoplasmic reticulum stress / Peptide ligand-binding receptors / calcium-mediated signaling / response to molecule of bacterial origin / receptor internalization / positive regulation of angiogenesis / chemotaxis / antimicrobial humoral immune response mediated by antimicrobial peptide / cellular response to tumor necrosis factor / heparin binding / cellular response to lipopolysaccharide / Senescence-Associated Secretory Phenotype (SASP) / angiogenesis / Interleukin-4 and Interleukin-13 signaling / G alpha (i) signalling events / intracellular signal transduction / G protein-coupled receptor signaling pathway / inflammatory response / negative regulation of cell population proliferation / negative regulation of gene expression / positive regulation of gene expression / signal transduction / extracellular space / extracellular region
Similarity search - Function
CXC chemokine / CXC chemokine, conserved site / Small cytokines (intercrine/chemokine) C-x-C subfamily signature. / CXC Chemokine domain / Chemokine beta/gamma/delta / Intercrine alpha family (small cytokine C-X-C) (chemokine CXC). / Chemokine interleukin-8-like domain / Chemokine interleukin-8-like superfamily / Small cytokines (intecrine/chemokine), interleukin-8 like / OB fold (Dihydrolipoamide Acetyltransferase, E2P) - #40 ...CXC chemokine / CXC chemokine, conserved site / Small cytokines (intercrine/chemokine) C-x-C subfamily signature. / CXC Chemokine domain / Chemokine beta/gamma/delta / Intercrine alpha family (small cytokine C-X-C) (chemokine CXC). / Chemokine interleukin-8-like domain / Chemokine interleukin-8-like superfamily / Small cytokines (intecrine/chemokine), interleukin-8 like / OB fold (Dihydrolipoamide Acetyltransferase, E2P) - #40 / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / Resolution: 2.01 Å
AuthorsEigenbrot, C. / Lowman, H.B. / Chee, L. / Artis, D.R.
Citation
Journal: Proteins / Year: 1997
Title: Structural change and receptor binding in a chemokine mutant with a rearranged disulfide: X-ray structure of E38C/C50AIL-8 at 2 A resolution.
Authors: Eigenbrot, C. / Lowman, H.B. / Chee, L. / Artis, D.R.
#1: Journal: Proc.Natl.Acad.Sci.USA / Year: 1991
Title: Crystal Structure of Interleukin 8: Symbiosis of NMR and Crystallography
Authors: Baldwin, E.T. / Weber, I.T. / Charles, R.St. / Xuan, J.C. / Appella, E. / Yamada, M. / Matsushima, K. / Edwards, B.F. / Clore, G.M. / Gronenborn, A.M. / al., et
History
DepositionSep 18, 1996Processing site: BNL
Revision 1.0Mar 12, 1997Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 3, 2021Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.4Nov 20, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: INTERLEUKIN-8
B: INTERLEUKIN-8


Theoretical massNumber of molelcules
Total (without water)16,6882
Polymers16,6882
Non-polymers00
Water93752
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1980 Å2
ΔGint-2 kcal/mol
Surface area7880 Å2
MethodPISA
Unit cell
Length a, b, c (Å)46.400, 49.200, 69.500
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein INTERLEUKIN-8 / IL-8


Mass: 8343.771 Da / Num. of mol.: 2 / Mutation: E38C, C50A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / References: UniProt: P10145
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 52 / 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: 2.38 Å3/Da / Density % sol: 42 %
Crystal grow
*PLUS
pH: 6.2 / Method: vapor diffusion, sitting drop
Details: protein solution is mixed in a 5:3 ratio with well solution
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
118 mg/mlprotein1drop
2250 mM1dropNaCl
310 mMMES1drop
430 %(w/v)PEG34001reservoir
50.1 Mammonium sulfate1reservoir

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Data collection

DiffractionMean temperature: 291 K
Diffraction sourceSource: ROTATING ANODE / Wavelength: 1.5418
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Jun 28, 1995
RadiationMonochromator: GRAPHITE(002) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.01→15 Å / Num. obs: 10544 / % possible obs: 96 % / Redundancy: 5 % / Rmerge(I) obs: 0.043 / Net I/σ(I): 27
Reflection shellResolution: 2.01→2.09 Å / Redundancy: 4 % / % possible all: 78
Reflection shell
*PLUS
% possible obs: 78 %

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Processing

Software
NameClassification
XDSdata scaling
X-PLORmodel building
X-PLORrefinement
XDSdata reduction
X-PLORphasing
RefinementResolution: 2.01→10 Å / σ(F): 2
RfactorNum. reflection% reflection
Rfree0.266 1000 9 %
Rwork0.194 --
obs0.194 8975 94 %
Displacement parametersBiso mean: 32 Å2
Refinement stepCycle: LAST / Resolution: 2.01→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1042 0 0 52 1094
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.01
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_deg1.57
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_it4.9
X-RAY DIFFRACTIONx_mcangle_it7.8
X-RAY DIFFRACTIONx_scbond_it7.7
X-RAY DIFFRACTIONx_scangle_it10.6
LS refinement shellResolution: 2.01→2.09 Å /
Rfactor% reflection
Rfree0.32 -
Rwork0.25 -
obs-70 %
Software
*PLUS
Name: X-PLOR / Classification: refinement
Refinement
*PLUS
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_deg23.9
X-RAY DIFFRACTIONx_improper_angle_deg1.19

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