+Open data
-Basic information
Entry | Database: PDB / ID: 2zkh | ||||||
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Title | Human thrombopoietin neutralizing antibody TN1 FAB | ||||||
Components |
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Keywords | IMMUNE SYSTEM / THROMBOPOIETIN / FAB FRAGMENT(ANTIBODY) | ||||||
Function / homology | Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta Function and homology information | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.04 Å | ||||||
Authors | Arai, S. / Tamada, T. / Honjo, E. / Maeda, Y. / Kuroki, R. | ||||||
Citation | Journal: Protein Sci. / Year: 2016 Title: An insight into the thermodynamic characteristics of human thrombopoietin complexation with TN1 antibody. Authors: Arai, S. / Shibazaki, C. / Adachi, M. / Honjo, E. / Tamada, T. / Maeda, Y. / Tahara, T. / Kato, T. / Miyazaki, H. / Blaber, M. / Kuroki, R. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2zkh.cif.gz | 98.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2zkh.ent.gz | 73 KB | Display | PDB format |
PDBx/mmJSON format | 2zkh.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2zkh_validation.pdf.gz | 433 KB | Display | wwPDB validaton report |
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Full document | 2zkh_full_validation.pdf.gz | 436.4 KB | Display | |
Data in XML | 2zkh_validation.xml.gz | 18.9 KB | Display | |
Data in CIF | 2zkh_validation.cif.gz | 27.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zk/2zkh ftp://data.pdbj.org/pub/pdb/validation_reports/zk/2zkh | HTTPS FTP |
-Related structure data
Related structure data | 2hrpS 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
#1: Antibody | Mass: 23362.854 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Cell (production host): Hybridoma cell / Production host: MUS MUSCULUS (house mouse) |
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#2: Antibody | Mass: 23364.170 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Cell (production host): Hybridoma cell / Production host: MUS MUSCULUS (house mouse) |
#3: 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: 2.3 Å3/Da / Density % sol: 46.55 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.2 Details: 0.2M potassium sodium tartrate, 20%W/V polyethylene glycol 3350, 19mg/ml protein concentration, pH 7.2, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: May 18, 2006 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.04→42.14 Å / Num. all: 27463 / Num. obs: 26573 / % possible obs: 98.97 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 5.5 % / Biso Wilson estimate: 24.01 Å2 / Rmerge(I) obs: 0.093 / Net I/σ(I): 10.3 |
Reflection shell | Resolution: 2.05→2.12 Å / Redundancy: 4.4 % / Rmerge(I) obs: 0.358 / Mean I/σ(I) obs: 6.6 / Num. unique all: 2647 / % possible all: 97.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2hrp Resolution: 2.04→42.14 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.929 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.208 / ESU R Free: 0.173 / 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: 25.127 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.04→42.14 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.037→2.09 Å / Total num. of bins used: 20
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