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Yorodumi- PDB-6itq: Crystal structure of cortisol complexed with its nanobody at pH 10.5 -
+Open data
-Basic information
Entry | Database: PDB / ID: 6itq | |||||||||
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Title | Crystal structure of cortisol complexed with its nanobody at pH 10.5 | |||||||||
Components | anti-cortisol camelid antibody | |||||||||
Keywords | IMMUNE SYSTEM / Cortisol / Complex / Nanobody / Camelid antibody | |||||||||
Function / homology | Chem-HCY Function and homology information | |||||||||
Biological species | Camelus bactrianus (Bactrian camel) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.526 Å | |||||||||
Authors | Ding, Y. / Ding, L.L. / Wang, Z.Y. / Zhong, P.Y. | |||||||||
Funding support | China, 2items
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Citation | Journal: Febs Lett. / Year: 2019 Title: Structural insights into the mechanism of single domain VHH antibody binding to cortisol. Authors: Ding, L. / Wang, Z. / Zhong, P. / Jiang, H. / Zhao, Z. / Zhang, Y. / Ren, Z. / Ding, Y. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6itq.cif.gz | 120.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6itq.ent.gz | 92.8 KB | Display | PDB format |
PDBx/mmJSON format | 6itq.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/it/6itq ftp://data.pdbj.org/pub/pdb/validation_reports/it/6itq | HTTPS FTP |
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-Related structure data
Related structure data | 6itpC 3k1kS S: Starting model for refinement C: citing same article (ref.) |
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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: 13780.096 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Camelus bactrianus (Bactrian camel) / Production host: Escherichia coli (E. coli) #2: Chemical | ChemComp-HCY / ( #3: Chemical | #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.13 Å3/Da / Density % sol: 42.15 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 10.5 Details: 2M Ammonium sulfate, 0.1M CAPS/Sodium hydroxide pH 10.5, 0.2M Lithium Sulfate |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | ||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.9792 Å | ||||||||||||||||||||||||
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Apr 29, 2018 | ||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9792 Å / Relative weight: 1 | ||||||||||||||||||||||||
Reflection | Resolution: 1.526→43.92 Å / Num. obs: 68100 / % possible obs: 96.7 % / Redundancy: 6.3 % / CC1/2: 0.916 / Rmerge(I) obs: 0.208 / Rpim(I) all: 0.095 / Rrim(I) all: 0.23 / Net I/σ(I): 7.7 | ||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Phasing
Phasing | Method: molecular replacement | |||||||||
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Phasing MR | Model details: Phaser MODE: MR_AUTO
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3K1K Resolution: 1.526→43.917 Å / SU ML: 0.21 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 25.92
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 48.38 Å2 / Biso mean: 16.6123 Å2 / Biso min: 3.59 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.526→43.917 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 23
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