+Open data
-Basic information
Entry | Database: PDB / ID: 3mbx | |||||||||
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Title | Crystal structure of chimeric antibody X836 | |||||||||
Components |
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Keywords | IMMUNE SYSTEM / IMMUNOGLOBULIN FOLD / MONOCLONAL ANTIBODY | |||||||||
Function / homology | Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta / PHOSPHATE ION Function and homology information | |||||||||
Biological species | Mus musculus (house mouse) Homo sapiens (human) | |||||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.6 Å | |||||||||
Authors | Teplyakov, A. / Obmolova, G. / Gilliland, G.L. | |||||||||
Citation | Journal: Mol.Immunol. / Year: 2010 Title: On the domain pairing in chimeric antibodies. Authors: Teplyakov, A. / Obmolova, G. / Carton, J.M. / Gao, W. / Zhao, Y. / Gilliland, G.L. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3mbx.cif.gz | 110.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3mbx.ent.gz | 82.2 KB | Display | PDB format |
PDBx/mmJSON format | 3mbx.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/mb/3mbx ftp://data.pdbj.org/pub/pdb/validation_reports/mb/3mbx | HTTPS FTP |
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-Related structure data
Related structure data | 1q9q 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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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Antibody | Mass: 24518.090 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) Cell (production host): Human embryonic kidney (HEK) 293 cells Production host: Homo sapiens (human) |
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#2: Antibody | Mass: 24763.795 Da / Num. of mol.: 1 Fragment: CHIMERIC MOLECULE OF MOUSE VARIABLE DOMAIN AND HUMAN CONSTANT DOMAIN, FD fragment Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus, Homo sapiens Cell (production host): Human embryonic kidney (HEK) 293 cells Production host: Homo sapiens (human) |
#3: Chemical | ChemComp-NA / |
#4: Chemical | ChemComp-PO4 / |
#5: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.76 Å3/Da / Density % sol: 55 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.2 Details: 0.1 M PHOSPHATE-CITRATE PH 4.2, 0.2 M SODIUM CHLORIDE, 10% PEG 3350; CRYO CONDITIONS: MOTHER LIQUOR + 20% GLYCEROL, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 118 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 / Wavelength: 1.5418 Å |
Detector | Type: RIGAKU SATURN 944 / Detector: CCD / Date: Jun 28, 2007 / Details: VARIMAX HF |
Radiation | Monochromator: NONE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.6→43.5 Å / Num. all: 69807 / Num. obs: 69807 / % possible obs: 96.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 8 % / Biso Wilson estimate: 24.5 Å2 / Rmerge(I) obs: 0.088 / Net I/σ(I): 12.6 |
Reflection shell | Resolution: 1.6→1.66 Å / Redundancy: 4.5 % / Rmerge(I) obs: 0.436 / Mean I/σ(I) obs: 3 / Num. unique all: 6545 / % possible all: 91.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1Q9Q 1q9q Resolution: 1.6→15 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.948 / SU B: 1.622 / SU ML: 0.058 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.092 / ESU R Free: 0.089 / Stereochemistry target values: Engh & Huber
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 28.7 Å2
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Refine analyze | Luzzati coordinate error obs: 0.09 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.6→15 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.6→1.641 Å / Total num. of bins used: 20
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