+Open data
-Basic information
Entry | Database: PDB / ID: 6wzl | ||||||
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Title | LY3041658 Fab bound to CXCL7 | ||||||
Components |
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Keywords | IMMUNE SYSTEM / CXCR1 / CXCR2 / neutrophil / NAP-2 | ||||||
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: 2.29 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 | 6wzl.cif.gz | 203.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6wzl.ent.gz | 159.7 KB | Display | PDB format |
PDBx/mmJSON format | 6wzl.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6wzl_validation.pdf.gz | 682.8 KB | Display | wwPDB validaton report |
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Full document | 6wzl_full_validation.pdf.gz | 686.6 KB | Display | |
Data in XML | 6wzl_validation.xml.gz | 35.6 KB | Display | |
Data in CIF | 6wzl_validation.cif.gz | 51.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wz/6wzl ftp://data.pdbj.org/pub/pdb/validation_reports/wz/6wzl | 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: 7684.054 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Macaca fascicularis (crab-eating macaque) Gene: EGM_14415 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A2K5UVV0, UniProt: G7P5K7*PLUS |
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-Antibody , 3 types, 4 molecules ABDC
#1: 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) | ||
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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: 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) |
-Non-polymers , 2 types, 207 molecules
#5: Chemical | ChemComp-PG6 / |
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#6: Water | ChemComp-HOH / |
-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: 2.77 Å3/Da / Density % sol: 55.52 % |
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Crystal grow | Temperature: 294 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 25% PEG 3000, 100mM Hepes pH 7.5 |
-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: Dec 12, 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: 2.29→60.79 Å / Num. obs: 51050 / % possible obs: 95.3 % / Redundancy: 3.7 % / Rmerge(I) obs: 0.069 / Net I/σ(I): 15.5 |
Reflection shell | Resolution: 2.29→2.42 Å / Rmerge(I) obs: 0.608 / Num. unique obs: 6892 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: Internal Resolution: 2.29→45.34 Å / Cor.coef. Fo:Fc: 0.94 / Cor.coef. Fo:Fc free: 0.926 / SU R Cruickshank DPI: 0.277 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.261 / SU Rfree Blow DPI: 0.194 / SU Rfree Cruickshank DPI: 0.2
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Displacement parameters | Biso max: 121.77 Å2 / Biso mean: 45.21 Å2 / Biso min: 20.64 Å2
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Refine analyze | Luzzati coordinate error obs: 0.3 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.29→45.34 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.29→2.31 Å / Rfactor Rfree error: 0 / Total num. of bins used: 50
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