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- PDB-1qe6: INTERLEUKIN-8 WITH AN ADDED DISULFIDE BETWEEN RESIDUES 5 AND 33 (... -

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Basic information

Entry
Database: PDB / ID: 1qe6
TitleINTERLEUKIN-8 WITH AN ADDED DISULFIDE BETWEEN RESIDUES 5 AND 33 (L5C/H33C)
ComponentsINTERLEUKIN-8 VARIANT
KeywordsIMMUNE SYSTEM / INTERCRINE ALPHA FAMILY
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 / positive regulation of neutrophil chemotaxis ...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 / positive regulation of neutrophil chemotaxis / chemokine activity / 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 / Peptide ligand-binding receptors / response to endoplasmic reticulum stress / 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 / SYNCHROTRON / Resolution: 2.35 Å
AuthorsGerber, N. / Lowman, H. / Artis, D.R. / Eigenbrot, C.
Citation
Journal: Proteins / Year: 2000
Title: Receptor-binding conformation of the "ELR" motif of IL-8: X-ray structure of the L5C/H33C variant at 2.35 A resolution.
Authors: Gerber, N. / Lowman, H. / Artis, D.R. / Eigenbrot, C.
#1: Journal: Proc.Natl.Acad.Sci.USA / Year: 1991
Title: Crystal structure of IL-8:Symbiosis of NMR and crystallography
Authors: Baldwin, E.T. / Weber, I.T. / Charles, R.St. / Xuan, J.-C.
#2: Journal: Proteins / Year: 1997
Title: Structural change and receptor binding in a chemokine mutant with a re- arranged disulfide: X-ray structure of E38C/C50A IL-8 at 2 A resolution.
Authors: Eigenbrot, C. / Lowman, H.B. / Chee, L. / Artis, D.R.
History
DepositionJul 13, 1999Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 22, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jan 31, 2018Group: Advisory / Experimental preparation
Category: exptl_crystal_grow / pdbx_unobs_or_zero_occ_atoms / pdbx_unobs_or_zero_occ_residues
Item: _exptl_crystal_grow.temp
Revision 1.4Nov 20, 2024Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / pdbx_unobs_or_zero_occ_atoms / pdbx_unobs_or_zero_occ_residues / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: INTERLEUKIN-8 VARIANT
B: INTERLEUKIN-8 VARIANT
C: INTERLEUKIN-8 VARIANT
D: INTERLEUKIN-8 VARIANT
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,7157
Polymers33,4274
Non-polymers2883
Water4,161231
1
A: INTERLEUKIN-8 VARIANT
B: INTERLEUKIN-8 VARIANT
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,8103
Polymers16,7142
Non-polymers961
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2160 Å2
ΔGint-16 kcal/mol
Surface area8410 Å2
MethodPISA
2
C: INTERLEUKIN-8 VARIANT
D: INTERLEUKIN-8 VARIANT
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,9064
Polymers16,7142
Non-polymers1922
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2320 Å2
ΔGint-24 kcal/mol
Surface area8650 Å2
MethodPISA
3
C: INTERLEUKIN-8 VARIANT
D: INTERLEUKIN-8 VARIANT
hetero molecules

A: INTERLEUKIN-8 VARIANT
B: INTERLEUKIN-8 VARIANT
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,7157
Polymers33,4274
Non-polymers2883
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_656-x+1,y+1/2,-z+11
Buried area5340 Å2
ΔGint-46 kcal/mol
Surface area16210 Å2
MethodPISA
Unit cell
Length a, b, c (Å)37.540, 71.770, 57.860
Angle α, β, γ (deg.)90.00, 90.46, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
INTERLEUKIN-8 VARIANT


Mass: 8356.787 Da / Num. of mol.: 4 / Mutation: L5C, H33C
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell: MONOCYTE / Production host: Escherichia coli (E. coli) / References: UniProt: P10145
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 231 / 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: 2.33 Å3/Da / Density % sol: 47.22 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 6.2
Details: NACL, AMMONIUM SULFATE, PEG 8000, pH 6.2, VAPOR DIFFUSION, HANGING DROP, temperature 19K
Crystal grow
*PLUS
Temperature: 20 ℃
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
14.2 mg/mlprotein1drop
2100 mM1dropNaCl
34 mMMES1drop
460 mMammonium sulfate1drop
518 %(w/v)PEG80001drop
6100 mMammonium sulfate1reservoir
730 %(w/v)PEG80001reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: A1 / Wavelength: 0.908
DetectorType: PRINCETON 1K / Detector: CCD / Date: Oct 15, 1996
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.908 Å / Relative weight: 1
ReflectionResolution: 2.35→50 Å / Num. all: 12843 / Num. obs: 12188 / % possible obs: 95 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.3 % / Biso Wilson estimate: 22.4 Å2 / Rmerge(I) obs: 0.088 / Net I/σ(I): 13
Reflection shellResolution: 2.35→2.43 Å / Redundancy: 2.1 % / Rmerge(I) obs: 0.113 / % possible all: 86

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Processing

Software
NameVersionClassification
MCCDATAdata collection
SCALEPACKdata scaling
X-PLORmodel building
X-PLOR3.851refinement
MCCDATAdata reduction
X-PLORphasing
RefinementResolution: 2.35→20 Å / Rfactor Rfree error: 0.009 / Data cutoff high absF: 100000 / Data cutoff low absF: 0.1 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 999.999 / Stereochemistry target values: ENGH AND HUBER
RfactorNum. reflection% reflectionSelection details
Rfree0.278 881 7.2 %SHELLS
Rwork0.208 ---
all0.211 12186 --
obs0.208 12186 94.8 %-
Displacement parametersBiso mean: 10.1 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.35 Å0.25 Å
Luzzati d res low-5 Å
Luzzati sigma a0.38 Å0.17 Å
Refinement stepCycle: LAST / Resolution: 2.35→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2264 0 15 231 2510
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_bond_d0.005
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
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d27.6
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d0.6
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it2.334
X-RAY DIFFRACTIONx_mcangle_it3.175
X-RAY DIFFRACTIONx_scbond_it4.976
X-RAY DIFFRACTIONx_scangle_it6.387
LS refinement shellResolution: 2.35→2.43 Å / Rfactor Rfree error: 0.033 / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.387 137 12.6 %
Rwork0.216 952 -
obs--86 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMTOPHCSDX.PRO
X-RAY DIFFRACTION2PARAM.SO4TOP.SO4
Software
*PLUS
Name: X-PLOR(ONLINE) / Version: 3.851 / Classification: refinement
Refinement
*PLUS
σ(F): 2 / % reflection Rfree: 7.2 % / Rfactor obs: 0.206 / Rfactor Rfree: 0.277
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 10.1 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_bond_d0.006
X-RAY DIFFRACTIONx_angle_deg1
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg27.6
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg0.61
X-RAY DIFFRACTIONx_mcbond_it4
X-RAY DIFFRACTIONx_scbond_it6
X-RAY DIFFRACTIONx_mcangle_it5
X-RAY DIFFRACTIONx_scangle_it7
LS refinement shell
*PLUS
Rfactor Rfree: 0.387 / % reflection Rfree: 12.6 % / Rfactor Rwork: 0.216

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