+Open data
-Basic information
Entry | Database: PDB / ID: 6h3h | ||||||
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Title | Fab fragment of antibody against fullerene C60 | ||||||
Components |
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Keywords | IMMUNE SYSTEM / ANTIBODY FAB FULLERENE C60 | ||||||
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: 1.92 Å | ||||||
Authors | Osipov, E.M. / Tikhonova, T.V. | ||||||
Funding support | Russian Federation, 1items
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Citation | Journal: Acta Naturae / Year: 2019 Title: Structure of the Anti-C60 Fullerene Antibody Fab Fragment: Structural Determinants of Fullerene Binding. Authors: Osipov, E.M. / Hendrickson, O.D. / Tikhonova, T.V. / Zherdev, A.V. / Solopova, O.N. / Sveshnikov, P.G. / Dzantiev, B.B. / Popov, V.O. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6h3h.cif.gz | 184.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6h3h.ent.gz | 145.8 KB | Display | PDB format |
PDBx/mmJSON format | 6h3h.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/h3/6h3h ftp://data.pdbj.org/pub/pdb/validation_reports/h3/6h3h | HTTPS FTP |
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-Related structure data
Related structure data | 1mfbS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
#1: Antibody | Mass: 23775.477 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / Organ: Spleen #2: Antibody | Mass: 23129.604 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / Organ: SPLEEN #3: Chemical | ChemComp-GOL / #4: Chemical | ChemComp-SO4 / #5: 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: 2.49 Å3/Da / Density % sol: 50.53 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 25 % w/v PEG 3350, 0.2 M (NH4)2SO4, 0.1 M Bis-Tris, pH 6.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: KURCHATOV SNC / Beamline: K4.4 / Wavelength: 0.98 Å |
Detector | Type: RAYONIX SX-165mm / Detector: CCD / Date: Feb 27, 2014 |
Radiation | Monochromator: Si / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 |
Reflection | Resolution: 1.91→28.83 Å / Num. obs: 69665 / % possible obs: 99.5 % / Redundancy: 5 % / CC1/2: 0.999 / Rrim(I) all: 0.084 / Net I/σ(I): 17.5 |
Reflection shell | Resolution: 1.91→2.02 Å / Redundancy: 4.8 % / Num. unique obs: 10963 / CC1/2: 0.83 / Rrim(I) all: 0.569 / % possible all: 97.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1MFB Resolution: 1.92→28.83 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.931 / SU B: 4.271 / SU ML: 0.119 / SU R Cruickshank DPI: 0.16 / Cross valid method: FREE R-VALUE / ESU R: 0.158 / ESU R Free: 0.149 / SU Rfree Cruickshank DPI: 0.149
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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 mean: 30.3 Å2
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Refinement step | Cycle: 1 / Resolution: 1.92→28.83 Å
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Refine LS restraints |
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