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- PDB-6wzk: LY3041658 Fab bound to CXCL3 -

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Basic information

Entry
Database: PDB / ID: 6wzk
TitleLY3041658 Fab bound to CXCL3
Components
  • (LY3041658 Fab heavy ...) x 2
  • C-X-C motif chemokine 3
  • LY3041658 Fab light chain
KeywordsIMMUNE SYSTEM / CXCR1 / CXCR2 / neutrophil / GRO-gamma
Function / homology
Function and homology information


chemokine activity / inflammatory response / immune response / extracellular space
Similarity search - Function
CXC chemokine / CXC chemokine, conserved site / Small cytokines (intercrine/chemokine) C-x-C subfamily signature. / CXC Chemokine domain / 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
ACETATE ION / C-X-C motif chemokine
Similarity search - Component
Biological speciesHomo sapiens (human)
Macaca fascicularis (crab-eating macaque)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 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

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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: C-X-C motif chemokine 3
F: C-X-C motif chemokine 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)112,35215
Polymers111,8346
Non-polymers5189
Water12,899716
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14560 Å2
ΔGint-64 kcal/mol
Surface area43300 Å2
MethodPISA
Unit cell
Length a, b, c (Å)62.017, 65.159, 281.747
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

#4: Protein C-X-C motif chemokine 3 / CXCL3


Mass: 8239.742 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Macaca fascicularis (crab-eating macaque)
Gene: CXCL3 / Production host: Escherichia coli (E. coli) / References: UniProt: Q0EAC1

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Antibody , 3 types, 4 molecules ABDC

#1: Antibody LY3041658 Fab heavy chain


Mass: 24251.984 Da / Num. of mol.: 1 / Fragment: pyroglutamic acid at N-terminus
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)
#3: Antibody LY3041658 Fab heavy chain


Mass: 24269.016 Da / Num. of mol.: 1
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 , 4 types, 725 molecules

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


Mass: 62.068 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C2H6O2
#6: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#7: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 716 / 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: 2.54 Å3/Da / Density % sol: 51.62 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 25% PEG 4000, 200mM Magnesium Chloride, 100mM MES pH 6.5

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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: 1.8→65.16 Å / Num. obs: 105131 / % possible obs: 98.6 % / Redundancy: 7.4 % / Rmerge(I) obs: 0.101 / Net I/σ(I): 15.9
Reflection shellResolution: 1.8→1.9 Å / Rmerge(I) obs: 0.727 / Num. unique obs: 15015

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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: 1.8→26.02 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.931 / SU R Cruickshank DPI: 0.11 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.115 / SU Rfree Blow DPI: 0.109 / SU Rfree Cruickshank DPI: 0.107
RfactorNum. reflection% reflectionSelection details
Rfree0.209 5244 4.99 %RANDOM
Rwork0.178 ---
obs0.18 105059 98.3 %-
Displacement parametersBiso max: 113.28 Å2 / Biso mean: 24.95 Å2 / Biso min: 7.57 Å2
Baniso -1Baniso -2Baniso -3
1--2.1945 Å20 Å20 Å2
2--3.197 Å20 Å2
3----1.0025 Å2
Refine analyzeLuzzati coordinate error obs: 0.23 Å
Refinement stepCycle: final / Resolution: 1.8→26.02 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7504 0 41 716 8261
Biso mean--29.44 29.91 -
Num. residues----997
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d2604SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes1350HARMONIC5
X-RAY DIFFRACTIONt_it7860HARMONIC20
X-RAY DIFFRACTIONt_nbd3SEMIHARMONIC5
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion1069SEMIHARMONIC5
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_contact9192SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d7860HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg10760HARMONIC21.1
X-RAY DIFFRACTIONt_omega_torsion3.84
X-RAY DIFFRACTIONt_other_torsion15.25
LS refinement shellResolution: 1.8→1.81 Å / Rfactor Rfree error: 0 / Total num. of bins used: 50
RfactorNum. reflection% reflection
Rfree0.2683 92 4.38 %
Rwork0.2102 2010 -
all0.2127 2102 -
obs--97.4 %

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