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- PDB-5xhf: Crystal structure of Trastuzumab Fab fragment bearing p-azido-L-p... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5xhf | ||||||
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Title | Crystal structure of Trastuzumab Fab fragment bearing p-azido-L-phenylalanine | ||||||
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![]() | IMMUNE SYSTEM / FAB | ||||||
Function / homology | Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta![]() | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Kuratani, M. / Yanagisawa, T. / Sakamoto, K. / Yokoyama, S. | ||||||
![]() | ![]() Title: Extensive Survey of Antibody Invariant Positions for Efficient Chemical Conjugation Using Expanded Genetic Codes. Authors: Kato, A. / Kuratani, M. / Yanagisawa, T. / Ohtake, K. / Hayashi, A. / Amano, Y. / Kimura, K. / Yokoyama, S. / Sakamoto, K. / Shiraishi, Y. | ||||||
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 172.9 KB | Display | ![]() |
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PDB format | ![]() | 137.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 458.9 KB | Display | ![]() |
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Full document | ![]() | 465.9 KB | Display | |
Data in XML | ![]() | 29.7 KB | Display | |
Data in CIF | ![]() | 39.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5xhgC ![]() 1n8zS C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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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: 23527.096 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Production host: ![]() ![]() #2: Antibody | Mass: 23425.180 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Production host: ![]() ![]() |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.51 Å3/Da / Density % sol: 51.01 % / Description: THE FILE CONTAINS FRIEDEL PAIRS. |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: PEG 20000, MES-Na |
-Data collection
Diffraction | Mean temperature: 99 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: RAYONIX MX300-HS / Detector: CCD / Date: Mar 13, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 3.2→50 Å / Num. obs: 14758 / % possible obs: 95.7 % / Redundancy: 1.3 % / Net I/σ(I): 2.45 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1N8Z Resolution: 3.205→42.443 Å / SU ML: 0.47 / Cross valid method: FREE R-VALUE / σ(F): 1.98 / Phase error: 32.76 / Details: THE FILE CONTAINS FRIEDEL PAIRS.
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.205→42.443 Å
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Refine LS restraints |
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LS refinement shell |
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