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Yorodumi- PDB-3g5z: Antibodies Specifically Targeting a Locally Misfolded Region of T... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3g5z | ||||||
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Title | Antibodies Specifically Targeting a Locally Misfolded Region of Tumor Associated EGFR | ||||||
Components |
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Keywords | IMMUNE SYSTEM / antibody | ||||||
Function / homology | Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta Function and homology information | ||||||
Biological species | Mus musculus (house mouse) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.6 Å | ||||||
Authors | Garrett, T.P.J. / Burgess, A.W. | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2009 Title: Antibodies specifically targeting a locally misfolded region of tumor associated EGFR Authors: Garrett, T.P.J. / Burgess, A.W. / Gan, H.K. / Luwor, R.B. / Cartwright, G. / Walker, F. / Orchard, S.G. / Clayton, A.H.A. / Nice, E.C. / Rothacker, J. / Catimel, B. / Cavenee, W.K. / Old, L. ...Authors: Garrett, T.P.J. / Burgess, A.W. / Gan, H.K. / Luwor, R.B. / Cartwright, G. / Walker, F. / Orchard, S.G. / Clayton, A.H.A. / Nice, E.C. / Rothacker, J. / Catimel, B. / Cavenee, W.K. / Old, L.J. / Stockert, E. / Ritter, G. / Adams, T.E. / Hoyne, P.A. / Wittrup, D. / Chao, G. / Cochran, J.R. / Luo, C. / Lou, M. / Huyton, T. / Xu, Y. / Fairlie, W.D. / Yao, S. / Scott, A.M. / Johns, T.G. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3g5z.cif.gz | 89.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3g5z.ent.gz | 73.4 KB | Display | PDB format |
PDBx/mmJSON format | 3g5z.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3g5z_validation.pdf.gz | 434.6 KB | Display | wwPDB validaton report |
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Full document | 3g5z_full_validation.pdf.gz | 445.7 KB | Display | |
Data in XML | 3g5z_validation.xml.gz | 18 KB | Display | |
Data in CIF | 3g5z_validation.cif.gz | 24.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/g5/3g5z ftp://data.pdbj.org/pub/pdb/validation_reports/g5/3g5z | HTTPS FTP |
-Related 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: 23229.438 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Cell (production host): HYBRIDOMA CELL / Production host: Mus musculus (house mouse) |
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#2: Antibody | Mass: 23347.928 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Cell (production host): HYBRIDOMA CELL / Production host: Mus musculus (house mouse) |
#3: Water | ChemComp-HOH / |
Sequence details | A SEQUENCE DATABASE REFERENCE FOR THIS PROTEIN DOES NOT CURRENTLY EXIST. |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.02 Å3/Da / Density % sol: 38.97 % |
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Crystal grow | Temperature: 293 K / Method: evaporation / pH: 9 Details: 0.2M NH4 acetate, 24% PEG6K, 0.1M Bis-tris propane, pH9.0, EVAPORATION, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU MICROMAX-007 |
Detector | Type: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Relative weight: 1 |
Reflection | Resolution: 2.8→50 Å / Num. obs: 9171 / % possible obs: 98.4 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Rmerge(I) obs: 0.14 |
Reflection shell | Resolution: 2.8→2.87 Å / Rmerge(I) obs: 0.332 / % possible all: 90.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.6→35.75 Å / Cor.coef. Fo:Fc: 0.919 / Cor.coef. Fo:Fc free: 0.825 / SU B: 32.739 / SU ML: 0.332 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R Free: 0.456 / 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: 33.986 Å2
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Refinement step | Cycle: LAST / Resolution: 2.6→35.75 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.6→2.668 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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