+Open data
-Basic information
Entry | Database: PDB / ID: 8sjk | ||||||
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Title | Pembrolizumab Caffeine crystal | ||||||
Components |
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Keywords | IMMUNE SYSTEM / CANCER / ANTIBODY / SUBCLASSES / IGG4 / MELANOMA / NSCLC | ||||||
Function / homology | sucrose / CAFFEINE Function and homology information | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.22 Å | ||||||
Authors | Larpent, P. / Codan, L. / Bothe, J.R. / Stueber, D. / Reichert, P. / Fischmann, T. / Su, Y. / Pabit, S. / Gupta, S. / Iuzzolino, L. / Cote, A. | ||||||
Funding support | United States, 1items
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Citation | Journal: Mol Pharm. / Year: 2024 Title: Small-Angle X-ray Scattering as a Powerful Tool for Phase and Crystallinity Assessment of Monoclonal Antibody Crystallites in Support of Batch Crystallization. Authors: Larpent, P. / Codan, L. / Bothe, J.R. / Iuzzolino, L. / Pabit, S. / Gupta, S. / Fischmann, T. / Su, Y. / Reichert, P. / Stueber, D. / Cote, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8sjk.cif.gz | 276 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8sjk.ent.gz | 220.8 KB | Display | PDB format |
PDBx/mmJSON format | 8sjk.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8sjk_validation.pdf.gz | 1.4 MB | Display | wwPDB validaton report |
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Full document | 8sjk_full_validation.pdf.gz | 1.4 MB | Display | |
Data in XML | 8sjk_validation.xml.gz | 26.3 KB | Display | |
Data in CIF | 8sjk_validation.cif.gz | 38.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/sj/8sjk ftp://data.pdbj.org/pub/pdb/validation_reports/sj/8sjk | HTTPS FTP |
-Related structure data
Similar structure data | Similarity search - Function & homologyF&H Search |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
-Antibody , 2 types, 2 molecules AB
#1: Antibody | Mass: 23768.449 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Mammalia (mammals) |
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#2: Antibody | Mass: 49166.047 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Mammalia (mammals) |
-Sugars , 2 types, 3 molecules
#3: Polysaccharide | 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[2-acetamido-2-deoxy- ...2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose Source method: isolated from a genetically manipulated source |
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#4: Polysaccharide |
-Non-polymers , 2 types, 301 molecules
#5: Chemical | ChemComp-CFF / |
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#6: Water | ChemComp-HOH / |
-Details
Has ligand of interest | Y |
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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: 2.99 Å3/Da / Density % sol: 58.9 % |
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Crystal grow | Temperature: 300 K / Method: vapor diffusion / pH: 6.8 Details: 0.1M Na HEPES pH 6.8 0.2%W/V Caffeine, 12% PEG3350, 3% DEXTRAN |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 1, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.22→40.81 Å / Num. obs: 33863 / % possible obs: 99.7 % / Redundancy: 8.7 % / CC1/2: 0.995 / Rmerge(I) obs: 0.138 / Rrim(I) all: 0.147 / Net I/σ(I): 14.1 |
Reflection shell | Resolution: 2.22→2.453 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.904 / Mean I/σ(I) obs: 1.3 / Num. unique obs: 2412 / CC1/2: 0.542 / Rpim(I) all: 0.048 / Rrim(I) all: 0.147 / % possible all: 15.1 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.22→40.81 Å / Cor.coef. Fo:Fc: 0.932 / Cor.coef. Fo:Fc free: 0.899 / Rfactor Rfree error: 0 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.323 / SU Rfree Blow DPI: 0.234
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Displacement parameters | Biso mean: 37.21 Å2
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Refine analyze | Luzzati coordinate error obs: 0.29 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: 1 / Resolution: 2.22→40.81 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.22→2.29 Å / Rfactor Rfree error: 0 / Total num. of bins used: 17
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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