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Yorodumi- PDB-8jza: Crystal structure of single domain antibody kt75 of human Thyrogl... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8jza | ||||||
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Title | Crystal structure of single domain antibody kt75 of human Thyroglobulin | ||||||
Components | single domain antibody kt75 of human Thyroglobulin | ||||||
Keywords | IMMUNE SYSTEM / single domain antibodies Thyroglobulin nanobodies | ||||||
Function / homology | ACETATE ION / : Function and homology information | ||||||
Biological species | Camelus dromedarius (Arabian camel) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.35 Å | ||||||
Authors | Mistry, H. / Kumarasamy, J. / Kumari, S. / Kulkarni, S.P. / Gupta, G.D. | ||||||
Funding support | India, 1items
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Citation | Journal: To Be Published Title: Crystal structure of single domain antibody kt75 of human Thyroglobulin Authors: Mistry, H. / Kumarasamy, J. / Kumari, S. / Kulkarni, S.P. / Gupta, G.D. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8jza.cif.gz | 104.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8jza.ent.gz | 77.8 KB | Display | PDB format |
PDBx/mmJSON format | 8jza.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8jza_validation.pdf.gz | 436 KB | Display | wwPDB validaton report |
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Full document | 8jza_full_validation.pdf.gz | 436 KB | Display | |
Data in XML | 8jza_validation.xml.gz | 8.3 KB | Display | |
Data in CIF | 8jza_validation.cif.gz | 10.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/jz/8jza ftp://data.pdbj.org/pub/pdb/validation_reports/jz/8jza | HTTPS FTP |
-Related structure data
Similar structure data | Similarity search - Function & homologyF&H Search |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Antibody | Mass: 14837.221 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Camelus dromedarius (Arabian camel) / Production host: Escherichia coli (E. coli) | ||||||
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#2: Chemical | #3: Chemical | ChemComp-K / | #4: Water | ChemComp-HOH / | Has ligand of interest | N | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2 Å3/Da / Density % sol: 38.6 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 4M K-acetate, 0.1 M sodium HEPES pH 7.0, 10% glycerol |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: RRCAT INDUS-2 / Beamline: PX-BL21 / Wavelength: 0.97777 Å |
Detector | Type: MAR CCD 165 mm / Detector: CCD / Date: Mar 2, 2022 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97777 Å / Relative weight: 1 |
Reflection | Resolution: 1.35→38.75 Å / Num. obs: 26851 / % possible obs: 100 % / Redundancy: 7.9 % / Biso Wilson estimate: 12.8 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.055 / Rpim(I) all: 0.021 / Rrim(I) all: 0.059 / Χ2: 0.98 / Net I/σ(I): 18 |
Reflection shell | Resolution: 1.35→1.37 Å / Redundancy: 7.8 % / Rmerge(I) obs: 0.916 / Mean I/σ(I) obs: 2.4 / Num. unique obs: 1329 / CC1/2: 0.764 / Rpim(I) all: 0.349 / Rrim(I) all: 0.981 / Χ2: 1.01 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.35→38.239 Å / Cor.coef. Fo:Fc: 0.979 / Cor.coef. Fo:Fc free: 0.972 / SU B: 1.824 / SU ML: 0.033 / Cross valid method: FREE R-VALUE / ESU R: 0.048 / ESU R Free: 0.05
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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 BULK SOLVENT | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 22.737 Å2
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Refinement step | Cycle: LAST / Resolution: 1.35→38.239 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20
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