+Open data
-Basic information
Entry | Database: PDB / ID: 6ug8 | |||||||||
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Title | Complex of ch28/11 Fab and SSEA-4 (monoclinic form) | |||||||||
Components |
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Keywords | IMMUNE SYSTEM / IMMUNOGLOBULIN / CHIMERIC ANTIBODY / ANTIGEN BINDING FRAGMENT / SSEA-4 / COMPLEX | |||||||||
Function / homology | Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta Function and homology information | |||||||||
Biological species | Mus musculus (house mouse) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.89 Å | |||||||||
Authors | Soliman, C. / Ramsland, P.A. | |||||||||
Citation | Journal: J.Biol.Chem. / Year: 2020 Title: The terminal sialic acid of stage-specific embryonic antigen-4 has a crucial role in binding to a cancer-targeting antibody. Authors: Soliman, C. / Chua, J.X. / Vankemmelbeke, M. / McIntosh, R.S. / Guy, A.J. / Spendlove, I. / Durrant, L.G. / Ramsland, P.A. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6ug8.cif.gz | 109.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6ug8.ent.gz | 79.1 KB | Display | PDB format |
PDBx/mmJSON format | 6ug8.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6ug8_validation.pdf.gz | 316.3 KB | Display | wwPDB validaton report |
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Full document | 6ug8_full_validation.pdf.gz | 316.7 KB | Display | |
Data in XML | 6ug8_validation.xml.gz | 1.6 KB | Display | |
Data in CIF | 6ug8_validation.cif.gz | 7.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ug/6ug8 ftp://data.pdbj.org/pub/pdb/validation_reports/ug/6ug8 | HTTPS FTP |
-Related structure data
Related structure data | 6ug7SC 6ug9C 6ugaC S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Antibody | Mass: 23166.750 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Cell line: Expi293 / Production host: Homo sapiens (human) |
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#2: Antibody | Mass: 23016.844 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Cell line (production host): Expi293 / Production host: Homo sapiens (human) |
#3: Polysaccharide | N-acetyl-alpha-neuraminic acid-(2-3)-beta-D-galactopyranose-(1-3)-2-acetamido-2-deoxy-beta-D- ...N-acetyl-alpha-neuraminic acid-(2-3)-beta-D-galactopyranose-(1-3)-2-acetamido-2-deoxy-beta-D-galactopyranose-(1-3)-alpha-D-galactopyranose-(1-4)-beta-D-galactopyranose-(1-4)-beta-D-glucopyranose Source method: isolated from a genetically manipulated source |
#4: Water | ChemComp-HOH / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.8 Å3/Da / Density % sol: 55.2 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.5 / Details: PEG 8000, sodium cacodylate, magnesium acetate |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.954 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Apr 16, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.954 Å / Relative weight: 1 |
Reflection | Resolution: 1.89→50 Å / Num. obs: 39580 / % possible obs: 99.3 % / Redundancy: 3.4 % / Rrim(I) all: 0.07 / Net I/σ(I): 10.1 |
Reflection shell | Resolution: 1.9→2 Å / Num. unique obs: 6187 / Rrim(I) all: 0.57 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6UG7 Resolution: 1.89→50 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.951 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.134 / ESU R Free: 0.138 Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 102.32 Å2 / Biso mean: 41.9978 Å2 / Biso min: 23.13 Å2
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Refinement step | Cycle: LAST / Resolution: 1.89→50 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.89→1.939 Å / Total num. of bins used: 20
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