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Yorodumi- PDB-6my4: Crystal structure of the dimeric bH1-Fab variant [HC-Y33W,HC-D98M... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6my4 | ||||||
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Title | Crystal structure of the dimeric bH1-Fab variant [HC-Y33W,HC-D98M,HC-G99M,LC-S30bR] | ||||||
Components |
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Keywords | IMMUNE SYSTEM / Fab fragment / antibody assembly / dimeric Fab | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.69 Å | ||||||
Authors | Shi, R. / Picard, M.-E. / Manenda, M. | ||||||
Funding support | Canada, 1items
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Citation | Journal: Mabs / Year: 2019 Title: Binding symmetry and surface flexibility mediate antibody self-association. Authors: Schrag, J.D. / Picard, M.E. / Gaudreault, F. / Gagnon, L.P. / Baardsnes, J. / Manenda, M.S. / Sheff, J. / Deprez, C. / Baptista, C. / Hogues, H. / Kelly, J.F. / Purisima, E.O. / Shi, R. / Sulea, T. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6my4.cif.gz | 204.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6my4.ent.gz | 160.2 KB | Display | PDB format |
PDBx/mmJSON format | 6my4.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/my/6my4 ftp://data.pdbj.org/pub/pdb/validation_reports/my/6my4 | HTTPS FTP |
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-Related structure data
Related structure data | 6mxrC 6mxsSC 6my5C 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: 25422.518 Da / Num. of mol.: 2 / Mutation: Y33W,D98M,G99M Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): CHO-3E7 / Production host: Cricetulus griseus (Chinese hamster) / References: UniProt: V9HW68 #2: Antibody | Mass: 24026.705 Da / Num. of mol.: 2 / Mutation: S30bR,S30bR Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): CHO-3E7 / Production host: Cricetulus griseus (Chinese hamster) / References: UniProt: Q7Z3Y4 #3: Chemical | ChemComp-EDO / #4: Water | ChemComp-HOH / | |
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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: 2.5 Å3/Da / Density % sol: 50.81 % |
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Crystal grow | Temperature: 295 K / Method: microbatch / pH: 8 / Details: 0.05 M imidazole, pH 8.0, 18% PEG6000 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | ||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.9795 Å | ||||||||||||||||||||||||
Detector | Type: RAYONIX MX-300 / Detector: CCD / Date: Jan 13, 2017 | ||||||||||||||||||||||||
Radiation | Monochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 | ||||||||||||||||||||||||
Reflection | Resolution: 1.69→50 Å / Num. obs: 108642 / % possible obs: 99.4 % / Redundancy: 3.8 % / CC1/2: 0.998 / Rmerge(I) obs: 0.067 / Rpim(I) all: 0.04 / Rrim(I) all: 0.078 / Net I/σ(I): 10.7 | ||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 6MXS Resolution: 1.69→50 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.947 / SU B: 2.562 / SU ML: 0.083 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.107 / ESU R Free: 0.109 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: 84.64 Å2 / Biso mean: 27.794 Å2 / Biso min: 9.78 Å2
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Refinement step | Cycle: final / Resolution: 1.69→50 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.69→1.734 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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