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Yorodumi- PDB-5xhg: Crystal structure of Trastuzumab Fab fragment bearing Ne-(o-azido... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5xhg | ||||||
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Title | Crystal structure of Trastuzumab Fab fragment bearing Ne-(o-azidobenzyloxycarbonyl)-L-lysine | ||||||
Components |
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Keywords | IMMUNE SYSTEM / FAB | ||||||
Function / homology | Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta / (2-azidophenyl)methyl hydrogen carbonate / DI(HYDROXYETHYL)ETHER Function and homology information | ||||||
Biological species | MUS MUSCULUS (house mouse) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.76 Å | ||||||
Authors | Kuratani, M. / Yanagisawa, T. / Sakamoto, K. / Yokoyama, S. | ||||||
Citation | Journal: Bioconjug. Chem. / Year: 2017 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. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5xhg.cif.gz | 361 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5xhg.ent.gz | 305.5 KB | Display | PDB format |
PDBx/mmJSON format | 5xhg.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5xhg_validation.pdf.gz | 505.2 KB | Display | wwPDB validaton report |
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Full document | 5xhg_full_validation.pdf.gz | 516.9 KB | Display | |
Data in XML | 5xhg_validation.xml.gz | 47.6 KB | Display | |
Data in CIF | 5xhg_validation.cif.gz | 72.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xh/5xhg ftp://data.pdbj.org/pub/pdb/validation_reports/xh/5xhg | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
-Antibody , 2 types, 4 molecules ACBD
#1: Antibody | Mass: 23467.082 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) MUS MUSCULUS (house mouse) / Description: humanized mouse Production host: Escherichia coli str. K-12 substr. W3110 (bacteria) #2: Antibody | Mass: 23425.180 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) MUS MUSCULUS (house mouse) / Description: humanized mouse Production host: Escherichia coli str. K-12 substr. W3110 (bacteria) |
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-Non-polymers , 5 types, 1275 molecules
#3: Chemical | ChemComp-OAZ / ( | ||||||
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#4: Chemical | #5: Chemical | ChemComp-EDO / #6: Chemical | #7: 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: 2.5 Å3/Da / Density % sol: 50.77 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / Details: Ammonium sulfate, PEG 3350, Bis-Tris |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSRRC / Beamline: BL15A1 / Wavelength: 1 Å |
Detector | Type: RAYONIX MX300HE / Detector: CCD / Date: Aug 4, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.76→30 Å / Num. obs: 230256 / % possible obs: 95.8 % / Redundancy: 1.3 % / Net I/σ(I): 7.92 |
-Processing
Software |
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Refinement | Resolution: 1.76→25.438 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 0.09 / Phase error: 20.73 / 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 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.76→25.438 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Origin x: 21.188 Å / Origin y: 63.57 Å / Origin z: 7.8992 Å
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Refinement TLS group | Selection details: all |