+Open data
-Basic information
Entry | Database: PDB / ID: 3if1 | ||||||
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Title | Crystal structure of 237mAb in complex with a GalNAc | ||||||
Components | (Immunoglobulin ...Antibody) x 2 | ||||||
Keywords | IMMUNE SYSTEM / glycopepitde / antibody / Fab / carbohydrate-biding / tumour | ||||||
Function / homology | Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta / 2-acetamido-2-deoxy-beta-D-galactopyranose Function and homology information | ||||||
Biological species | Mus musculus (house mouse) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.39 Å | ||||||
Authors | Brooks, C.L. / Evans, S.V. / Borisova, S.N. | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2010 Title: Antibody recognition of a unique tumor-specific glycopeptide antigen. Authors: Brooks, C.L. / Schietinger, A. / Borisova, S.N. / Kufer, P. / Okon, M. / Hirama, T. / Mackenzie, C.R. / Wang, L.X. / Schreiber, H. / Evans, S.V. #1: Journal: Science / Year: 2006 Title: A mutant chaperone converts a wild-type protein into a tumor-specific antigen Authors: Schietinger, A. / Philip, M. / Yoshida, B.A. / Azadi, P. / Liu, H. / Meredith, S.C. / Schreiber, H. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3if1.cif.gz | 185.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3if1.ent.gz | 144.5 KB | Display | PDB format |
PDBx/mmJSON format | 3if1.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/if/3if1 ftp://data.pdbj.org/pub/pdb/validation_reports/if/3if1 | HTTPS FTP |
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-Related structure data
Related structure data | 3ietSC 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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2 |
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3 |
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Unit cell |
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Components on special symmetry positions |
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-Components
-Antibody , 2 types, 4 molecules ACBD
#1: Antibody | Mass: 23591.104 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Strain: BALB/c / Production host: Mus musculus (house mouse) #2: Antibody | Mass: 23409.178 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Strain: BALB/c / Production host: Mus musculus (house mouse) |
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-Sugars , 1 types, 2 molecules
#5: Sugar |
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-Non-polymers , 3 types, 433 molecules
#3: Chemical | ChemComp-ZN / #4: Chemical | ChemComp-MG / #6: 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: 2.59 Å3/Da / Density % sol: 52.49 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: PEG MME 5000, ZnCl2, MgCl2, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU MICROMAX-002+ / Wavelength: 1.5418 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Jun 10, 2007 / Details: mirrors | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: Ni FILTER / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.39→19.93 Å / Num. obs: 38606 / % possible obs: 99 % / Redundancy: 3.42 % / Rmerge(I) obs: 0.073 / Χ2: 0.85 / Net I/σ(I): 8.4 / Scaling rejects: 2071 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3IET Resolution: 2.39→19.93 Å / Occupancy max: 1 / Occupancy min: 1 / SU ML: 1.08 / σ(F): 1.34 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 42.114 Å2 / ksol: 0.368 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 84.43 Å2 / Biso mean: 31.035 Å2 / Biso min: 5.71 Å2
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Refinement step | Cycle: LAST / Resolution: 2.39→19.93 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 14
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