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- PDB-6wzj: LY3041658 Fab bound to CXCL2 -

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Basic information

Entry
Database: PDB / ID: 6wzj
TitleLY3041658 Fab bound to CXCL2
Components
  • C-X-C motif chemokine 2
  • LY3041658 Fab Heavy Chain
  • LY3041658 Fab Light Chain
KeywordsIMMUNE SYSTEM / CXCR1 / CXCR2 / neutrophil / GRO-beta
Function / homology
Function and homology information


chemokine activity / immune response / inflammatory 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
C-X-C motif chemokine
Similarity search - Component
Biological speciesHomo sapiens (human)
Macaca fascicularis (crab-eating macaque)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.37 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 2
F: C-X-C motif chemokine 2


Theoretical massNumber of molelcules
Total (without water)110,9906
Polymers110,9906
Non-polymers00
Water4,089227
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)56.042, 200.643, 65.253
Angle α, β, γ (deg.)90.000, 106.680, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#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)
#3: Protein C-X-C motif chemokine 2 / CXCL2


Mass: 7809.251 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Macaca fascicularis (crab-eating macaque)
Gene: CXCL2 / Production host: Escherichia coli (E. coli) / References: UniProt: Q0EAC2
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 227 / 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: 3.17 Å3/Da / Density % sol: 61.15 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: 12% PEG 20000, 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 5, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97931 Å / Relative weight: 1
ReflectionResolution: 2.37→19.92 Å / Num. obs: 55547 / % possible obs: 99.6 % / Redundancy: 3.8 % / Rmerge(I) obs: 0.101 / Net I/σ(I): 5.9
Reflection shellResolution: 2.37→2.5 Å / Rmerge(I) obs: 0.81 / Num. unique obs: 8122

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Processing

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

Resolution: 2.37→19.89 Å / Cor.coef. Fo:Fc: 0.931 / Cor.coef. Fo:Fc free: 0.918 / SU R Cruickshank DPI: 0.279 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.268 / SU Rfree Blow DPI: 0.206 / SU Rfree Cruickshank DPI: 0.212
RfactorNum. reflection% reflectionSelection details
Rfree0.242 1731 3.12 %RANDOM
Rwork0.215 ---
obs0.215 55515 99.7 %-
Displacement parametersBiso max: 133.27 Å2 / Biso mean: 57.27 Å2 / Biso min: 24.09 Å2
Baniso -1Baniso -2Baniso -3
1--2.3723 Å20 Å2-6.707 Å2
2--7.7628 Å20 Å2
3----5.3906 Å2
Refine analyzeLuzzati coordinate error obs: 0.37 Å
Refinement stepCycle: final / Resolution: 2.37→19.89 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7361 0 0 227 7588
Biso mean---49.68 -
Num. residues----991
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d2413SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes1271HARMONIC5
X-RAY DIFFRACTIONt_it7542HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion1016SEMIHARMONIC5
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_contact7925SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d7542HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg10302HARMONIC21.2
X-RAY DIFFRACTIONt_omega_torsion3.42
X-RAY DIFFRACTIONt_other_torsion17.69
LS refinement shellResolution: 2.37→2.39 Å / Rfactor Rfree error: 0 / Total num. of bins used: 50
RfactorNum. reflection% reflection
Rfree0.3054 36 3.24 %
Rwork0.2348 1075 -
all0.2371 1111 -
obs--99.26 %

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