[English] 日本語
Yorodumi- PDB-6itp: Crystal structure of cortisol complexed with its nanobody at pH 3.5 -
+Open data
-Basic information
Entry | Database: PDB / ID: 6itp | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | Crystal structure of cortisol complexed with its nanobody at pH 3.5 | |||||||||
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: 1.572 Å | |||||||||
Authors | Ding, Y. / Ding, L.L. / Wang, Z.Y. / Zhong, P.Y. | |||||||||
Funding support | China, 2items
| |||||||||
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 |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 6itp.cif.gz | 112.4 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb6itp.ent.gz | 86.3 KB | Display | PDB format |
PDBx/mmJSON format | 6itp.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6itp_validation.pdf.gz | 1 MB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 6itp_full_validation.pdf.gz | 1 MB | Display | |
Data in XML | 6itp_validation.xml.gz | 16.3 KB | Display | |
Data in CIF | 6itp_validation.cif.gz | 23.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/it/6itp ftp://data.pdbj.org/pub/pdb/validation_reports/it/6itp | HTTPS FTP |
-Related structure data
Related structure data | 6itqC 3k1kS S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| |||||||||
---|---|---|---|---|---|---|---|---|---|---|
1 |
| |||||||||
Unit cell |
| |||||||||
Components on special symmetry positions |
|
-Components
#1: Antibody | Mass: 13780.096 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Camelus bactrianus (Bactrian camel) / Production host: Escherichia coli (E. coli) #2: Chemical | #3: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.6 Å3/Da / Density % sol: 52.62 % |
---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 3.5 / Details: 0.1M Citric acid pH 3.5, 3M NaCl |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.9793 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Nov 12, 2018 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9793 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.57→50 Å / Num. obs: 40074 / % possible obs: 99.8 % / Redundancy: 39.5 % / Biso Wilson estimate: 13.36 Å2 / Rmerge(I) obs: 0.08 / Rpim(I) all: 0.013 / Rrim(I) all: 0.081 / Χ2: 0.791 / Net I/σ(I): 4.5 / Num. measured all: 1584876 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
|
-Phasing
Phasing | Method: molecular replacement | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Phasing MR | Model details: Phaser MODE: MR_AUTO
|
-Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3K1K Resolution: 1.572→33.603 Å / SU ML: 0.14 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 21.47
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 77.6 Å2 / Biso mean: 20.1569 Å2 / Biso min: 5.37 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.572→33.603 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14
|