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- PDB-4xdx: The crystal structure of soluble human interleukin 8 expressed in... -

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Basic information

Entry
Database: PDB / ID: 4xdx
TitleThe crystal structure of soluble human interleukin 8 expressed in Pichia pastoris
ComponentsInterleukin-8Interleukin 8
KeywordsCYTOKINE / alpha beta protein / IL8 fold / 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 / positive regulation of cellular biosynthetic process / negative regulation of cell adhesion molecule production / negative regulation of G protein-coupled receptor signaling pathway / ATF4 activates genes in response to endoplasmic reticulum stress / CXCR chemokine receptor binding / embryonic digestive tract development / neutrophil activation ...regulation of single stranded viral RNA replication via double stranded DNA intermediate / regulation of entry of bacterium into host cell / interleukin-8 receptor binding / positive regulation of cellular biosynthetic process / negative regulation of cell adhesion molecule production / negative regulation of G protein-coupled receptor signaling pathway / ATF4 activates genes in response to endoplasmic reticulum stress / CXCR chemokine receptor binding / embryonic digestive tract development / neutrophil activation / induction of positive chemotaxis / cellular response to fibroblast growth factor stimulus / chemokine-mediated signaling pathway / positive regulation of neutrophil chemotaxis / Chemokine receptors bind chemokines / chemokine activity / Interleukin-10 signaling / cellular response to interleukin-1 / regulation of cell adhesion / response to endoplasmic reticulum stress / Peptide ligand-binding receptors / neutrophil chemotaxis / calcium-mediated signaling / response to molecule of bacterial origin / receptor internalization / positive regulation of angiogenesis / chemotaxis / antimicrobial humoral immune response mediated by antimicrobial peptide / heparin binding / cellular response to tumor necrosis factor / G alpha (i) signalling events / Senescence-Associated Secretory Phenotype (SASP) / angiogenesis / Interleukin-4 and Interleukin-13 signaling / cellular response to lipopolysaccharide / intracellular signal transduction / inflammatory response / G protein-coupled receptor signaling pathway / 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 / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 0.95 Å
AuthorsOstrov, D.A. / Pompeu, Y.A. / Jakoncic, J.J.
CitationJournal: To Be Published
Title: The crystal structure of soluble human interleukin 8 expressed in Pichia pastoris
Authors: Ostrov, D.A. / Pompeu, Y.A. / Jakoncic, J.J.
History
DepositionDec 20, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 23, 2015Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2017Group: Derived calculations / Refinement description / Category: pdbx_struct_oper_list / software
Item: _pdbx_struct_oper_list.symmetry_operation / _software.classification / _software.name
Revision 1.2Sep 27, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
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-8


Theoretical massNumber of molelcules
Total (without water)8,2441
Polymers8,2441
Non-polymers00
Water2,540141
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area5310 Å2
MethodPISA
Unit cell
Length a, b, c (Å)40.093, 40.093, 89.269
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein Interleukin-8 / Interleukin 8 / IL-8 / C-X-C motif chemokine 8 / Chemokine (C-X-C motif) ligand 8 / Emoctakin / Granulocyte ...IL-8 / C-X-C motif chemokine 8 / Chemokine (C-X-C motif) ligand 8 / Emoctakin / Granulocyte chemotactic protein 1 / GCP-1 / Monocyte-derived neutrophil chemotactic factor / MDNCF / Monocyte-derived neutrophil-activating peptide / MONAP / Neutrophil-activating protein 1 / NAP-1 / Protein 3-10C / T-cell chemotactic factor


Mass: 8243.651 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CXCL8, IL8 / Production host: Komagataella pastoris (fungus) / References: UniProt: P10145
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 141 / Source method: isolated from a natural source / Formula: H2O

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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: 2.51 Å3/Da / Density % sol: 51.04 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: 0.17 M Ammonium acetate, 0.085 M Sodium citrate tribasic dihydrate pH 5.6, 20% w/v Polyethylene glycol 4,000, 15% v/v Glycerol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X6A / Wavelength: 0.806 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Aug 21, 2009
RadiationMonochromator: Si(111) Channel-Cut / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.806 Å / Relative weight: 1
ReflectionResolution: 0.95→8 Å / Num. obs: 52929 / % possible obs: 99.5 % / Redundancy: 8.7 % / Biso Wilson estimate: 8.52 Å2 / Rmerge(I) obs: 0.05 / Net I/σ(I): 37.81
Reflection shellResolution: 0.95→0.97 Å / Redundancy: 8.5 % / Rmerge(I) obs: 0.743 / Mean I/σ(I) obs: 2.3 / % possible all: 100

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine: 1.9_1692)refinement
HKL-2000data reduction
Cootmodel building
PDB_EXTRACT3.14data extraction
HKL-2000data scaling
PHASERphasing
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3il8

3il8


Resolution: 0.95→7.939 Å / SU ML: 0.07 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 10.72 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1356 2635 5 %random
Rwork0.1208 50065 --
obs0.1216 52700 99.21 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 55.08 Å2 / Biso mean: 15.1823 Å2 / Biso min: 6.06 Å2
Refinement stepCycle: final / Resolution: 0.95→7.939 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms571 0 6 141 718
Biso mean--26.72 30.3 -
Num. residues----70
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.025708
X-RAY DIFFRACTIONf_angle_d2.132971
X-RAY DIFFRACTIONf_chiral_restr0.106107
X-RAY DIFFRACTIONf_plane_restr0.014126
X-RAY DIFFRACTIONf_dihedral_angle_d13.319317
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 19

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
0.9501-0.96730.22621320.21392432256494
0.9673-0.98590.21131360.17392570270699
0.9859-1.0060.16281400.146626522792100
1.006-1.02780.15231370.126326502787100
1.0278-1.05170.1481370.115726112748100
1.0517-1.07790.1251390.110225932732100
1.0779-1.1070.12041350.091426212756100
1.107-1.13950.1241450.09326452790100
1.1395-1.17610.11221370.088526502787100
1.1761-1.2180.10261410.089726172758100
1.218-1.26660.11451370.089226312768100
1.2666-1.3240.11171380.090326422780100
1.324-1.39350.11551380.096526762814100
1.3935-1.48020.12711410.096326572798100
1.4802-1.59370.11241400.096626712811100
1.5937-1.75250.11731380.103926742812100
1.7525-2.00250.12211440.116127142858100
2.0025-2.50970.14141450.129527162861100
2.5097-7.93910.16421350.162643277893

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