+Open data
-Basic information
Entry | Database: PDB / ID: 6wzk | ||||||
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Title | LY3041658 Fab bound to CXCL3 | ||||||
Components |
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Keywords | IMMUNE SYSTEM / CXCR1 / CXCR2 / neutrophil / GRO-gamma | ||||||
Function / homology | Function and homology information chemokine activity / inflammatory response / immune response / extracellular space Similarity search - Function | ||||||
Biological species | Homo sapiens (human) Macaca fascicularis (crab-eating macaque) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å | ||||||
Authors | Durbin, J.D. / Druzina, Z. | ||||||
Citation | Journal: 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 |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6wzk.cif.gz | 221.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6wzk.ent.gz | 172.9 KB | Display | PDB format |
PDBx/mmJSON format | 6wzk.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6wzk_validation.pdf.gz | 485.4 KB | Display | wwPDB validaton report |
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Full document | 6wzk_full_validation.pdf.gz | 488.7 KB | Display | |
Data in XML | 6wzk_validation.xml.gz | 42.7 KB | Display | |
Data in CIF | 6wzk_validation.cif.gz | 62.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wz/6wzk ftp://data.pdbj.org/pub/pdb/validation_reports/wz/6wzk | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
-Protein , 1 types, 2 molecules EF
#4: Protein | 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 | 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) | ||
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#2: Antibody | 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 | | 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) |
-Non-polymers , 4 types, 725 molecules
#5: Chemical | ChemComp-EDO / #6: Chemical | ChemComp-ACT / | #7: Chemical | ChemComp-MG / | #8: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | N |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.54 Å3/Da / Density % sol: 51.62 % |
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Crystal grow | Temperature: 294 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: 25% PEG 4000, 200mM Magnesium Chloride, 100mM MES pH 6.5 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 31-ID / Wavelength: 0.97931 Å |
Detector | Type: RAYONIX MX-225 / Detector: CCD / Date: Nov 10, 2011 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97931 Å / Relative weight: 1 |
Reflection | Resolution: 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 shell | Resolution: 1.8→1.9 Å / Rmerge(I) obs: 0.727 / Num. unique obs: 15015 |
-Processing
Software |
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Refinement | Method 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
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Displacement parameters | Biso max: 113.28 Å2 / Biso mean: 24.95 Å2 / Biso min: 7.57 Å2
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Refine analyze | Luzzati coordinate error obs: 0.23 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.8→26.02 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.8→1.81 Å / Rfactor Rfree error: 0 / Total num. of bins used: 50
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