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- PDB-6wzm: LY3041658 Fab bound to CXCL8 -

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Basic information

Entry
Database: PDB / ID: 6wzm
TitleLY3041658 Fab bound to CXCL8
Components
  • (LY3041658 Fab ...) x 2
  • Interleukin-8
KeywordsIMMUNE SYSTEM / CXCR1 / CXCR2 / neutrophil / interleukin-8
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 / induction of positive 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 / 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 / induction of positive chemotaxis / neutrophil activation / 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 / antimicrobial humoral immune response mediated by antimicrobial peptide / positive regulation of angiogenesis / chemotaxis / cellular response to tumor necrosis factor / heparin binding / G alpha (i) signalling events / Senescence-Associated Secretory Phenotype (SASP) / cellular response to lipopolysaccharide / angiogenesis / Interleukin-4 and Interleukin-13 signaling / 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
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.28 Å
AuthorsDurbin, J.D. / Druzina, Z.
CitationJournal: Mabs
Title: Discovery and characterization of a neutralizing pan-ELR+CXC chemokine monoclonal antibody.
Authors: Boyles, J.S. / Beidler, C.B. / Strifler, B.A. / Girard, D.S. / Druzina, Z. / Durbin, J.D. / Swearingen, M.L. / Lee, L.N. / Kikly, K. / Chintharlapalli, S. / Witcher, D.R.
History
DepositionMay 14, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 25, 2020Provider: repository / Type: Initial release
Revision 1.1Apr 3, 2024Group: 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: LY3041658 Fab heavy chain
B: LY3041658 Fab light chain
C: LY3041658 Fab heavy chain
D: LY3041658 Fab light chain
E: Interleukin-8
F: Interleukin-8
hetero molecules


Theoretical massNumber of molelcules
Total (without water)111,0568
Polymers110,8006
Non-polymers2562
Water9,350519
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)65.012, 103.629, 193.289
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 2 molecules EF

#3: Protein Interleukin-8 / IL-8 / CXCL8 / C-X-C motif chemokine 8 / Chemokine (C-X-C motif) ligand 8 / Emoctakin / Granulocyte ...IL-8 / CXCL8 / 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: 7714.061 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CXCL8, IL8 / Production host: Escherichia coli (E. coli) / References: UniProt: P10145

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Antibody , 2 types, 4 molecules ACBD

#1: Antibody LY3041658 Fab heavy chain


Mass: 24269.016 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#2: Antibody LY3041658 Fab light chain


Mass: 23416.926 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)

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Non-polymers , 3 types, 521 molecules

#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 519 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN

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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: 2.94 Å3/Da / Density % sol: 58.14 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / Details: 20% PEG 3350, 200mM Magnesium Chloride

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 31-ID / Wavelength: 0.97931 Å
DetectorType: RAYONIX MX-225 / Detector: CCD / Date: Nov 10, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97931 Å / Relative weight: 1
ReflectionResolution: 2.28→193.29 Å / Num. obs: 60358 / % possible obs: 99.8 % / Redundancy: 7.3 % / Rmerge(I) obs: 0.101 / Net I/σ(I): 15.8
Reflection shellResolution: 2.28→2.4 Å / Rmerge(I) obs: 0.637 / Num. unique obs: 8751

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Processing

Software
NameVersionClassification
BUSTER2.11.7refinement
PDB_EXTRACT3.25data extraction
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Internal

Resolution: 2.28→96.64 Å / Cor.coef. Fo:Fc: 0.94 / Cor.coef. Fo:Fc free: 0.914 / SU R Cruickshank DPI: 0.232 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.244 / SU Rfree Blow DPI: 0.194 / SU Rfree Cruickshank DPI: 0.192
RfactorNum. reflection% reflectionSelection details
Rfree0.229 2947 4.89 %RANDOM
Rwork0.187 ---
obs0.189 60269 99.7 %-
Displacement parametersBiso max: 125.61 Å2 / Biso mean: 40.21 Å2 / Biso min: 11.89 Å2
Baniso -1Baniso -2Baniso -3
1--1.5365 Å20 Å20 Å2
2---3.2229 Å20 Å2
3---4.7594 Å2
Refine analyzeLuzzati coordinate error obs: 0.29 Å
Refinement stepCycle: final / Resolution: 2.28→96.64 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7632 0 17 519 8168
Biso mean--50.81 41.94 -
Num. residues----1001
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d2584SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes1309HARMONIC5
X-RAY DIFFRACTIONt_it7846HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion1038SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact8647SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d7846HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg10686HARMONIC21.14
X-RAY DIFFRACTIONt_omega_torsion3.44
X-RAY DIFFRACTIONt_other_torsion17.46
LS refinement shellResolution: 2.28→2.3 Å / Rfactor Rfree error: 0 / Total num. of bins used: 50
RfactorNum. reflection% reflection
Rfree0.2963 60 4.98 %
Rwork0.2316 1146 -
all0.2347 1206 -
obs--98.55 %

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