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Yorodumi- PDB-3gkw: Crystal structure of the Fab fragment of Nimotuzumab. An anti-epi... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3gkw | ||||||
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Title | Crystal structure of the Fab fragment of Nimotuzumab. An anti-epidermal growth factor receptor antibody | ||||||
Components |
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Keywords | IMMUNE SYSTEM / ANTITUMOR PROTEIN / Immunoglobulin fold / Displaced strictly conserved TRP 103 following Kabat numbering | ||||||
Function / homology | Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta / DI(HYDROXYETHYL)ETHER Function and homology information | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å | ||||||
Authors | Talavera, A. / Friemann, R. / Martinez-Fleites, C. / Moreno, E. / Krengel, U. | ||||||
Citation | Journal: Cancer Res. / Year: 2009 Title: Nimotuzumab, an antitumor antibody that targets the epidermal growth factor receptor, blocks ligand binding while permitting the active receptor conformation Authors: Talavera, A. / Friemann, R. / Gomez-Puerta, S. / Martinez-Fleites, C. / Garrido, G. / Rabasa, A. / Lopez-Requena, A. / Pupo, A. / Johansen, R.F. / Sanchez, O. / Krengel, U. / Moreno, E. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3gkw.cif.gz | 97.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3gkw.ent.gz | 71.8 KB | Display | PDB format |
PDBx/mmJSON format | 3gkw.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gk/3gkw ftp://data.pdbj.org/pub/pdb/validation_reports/gk/3gkw | HTTPS FTP |
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-Related structure data
Related structure data | 1uywS 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: 23717.328 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: Humanized antibody by CDR grafting from a mouse source Source: (gene. exp.) Homo sapiens (human) / Cell line: B cell / Gene: Immonoglobulin / Plasmid: pcDNA3 / Cell line (production host): NSO / Production host: Mus musculus (house mouse) |
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#2: Antibody | Mass: 24182.740 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: Humanized antibody by CDR grafting from a mouse source Source: (gene. exp.) Homo sapiens (human) / Cell line: B cell / Gene: Immonoglobulin / Plasmid: pcDNA3 / Cell line (production host): NSO / Production host: Mus musculus (house mouse) |
#3: Chemical | ChemComp-PEG / |
#4: Chemical | ChemComp-1PE / |
#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: 2.56 Å3/Da / Density % sol: 52.04 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.75 Details: 0.1 M MES, 25% PEG 1000, pH 6.75, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: MAX II / Beamline: I711 / Wavelength: 0.97 Å |
Detector | Type: MAR CCD 165 mm / Detector: CCD / Date: Nov 5, 2003 / Details: mirror |
Radiation | Monochromator: cut single Si(111) crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→20 Å / Num. all: 17556 / Num. obs: 17486 / % possible obs: 98 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 7 % / Rmerge(I) obs: 0.125 / Net I/σ(I): 16.7 |
Reflection shell | Resolution: 2.5→2.56 Å / Redundancy: 6.8 % / Rmerge(I) obs: 0.489 / Mean I/σ(I) obs: 3.6 / % possible all: 98 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 1uyw Resolution: 2.5→19.79 Å / Cor.coef. Fo:Fc: 0.911 / Cor.coef. Fo:Fc free: 0.83 / SU B: 21.529 / SU ML: 0.226 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.527 / ESU R Free: 0.322 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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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: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 15.43 Å2
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Refinement step | Cycle: LAST / Resolution: 2.5→19.79 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.5→2.564 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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