[English] 日本語
Yorodumi- PDB-2xn5: Crystal structure of thyroxine-binding globulin complexed with Fu... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2xn5 | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of thyroxine-binding globulin complexed with Furosemide | ||||||
Components | (THYROXINE-BINDING ...) x 2 | ||||||
Keywords | TRANSPORT / CLEAVED PROTEIN | ||||||
Function / homology | Function and homology information thyroid hormone transport / serine-type endopeptidase inhibitor activity / extracellular space / extracellular exosome / extracellular region Similarity search - Function | ||||||
Biological species | HOMO SAPIENS (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å | ||||||
Authors | Qi, X. / Yan, Y. / Wei, Z. / Zhou, A. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2011 Title: Allosteric Modulation of Hormone Release from Thyroxine and Corticosteroid Binding-Globulins. Authors: Qi, X. / Loiseau, F. / Chan, W.L. / Yan, Y. / Wei, Z. / Milroy, L.G. / Myers, R.M. / Ley, S.V. / Read, R.J. / Carrell, R.W. / Zhou, A. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 2xn5.cif.gz | 168.8 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb2xn5.ent.gz | 131.4 KB | Display | PDB format |
PDBx/mmJSON format | 2xn5.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2xn5_validation.pdf.gz | 821 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 2xn5_full_validation.pdf.gz | 823.2 KB | Display | |
Data in XML | 2xn5_validation.xml.gz | 18.6 KB | Display | |
Data in CIF | 2xn5_validation.cif.gz | 27.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xn/2xn5 ftp://data.pdbj.org/pub/pdb/validation_reports/xn/2xn5 | HTTPS FTP |
-Related structure data
Related structure data | 2rivSC 2riwC 2xn3C 2xn6C 2xn7C C: citing same article (ref.) S: Starting model for refinement |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
| ||||||||
Components on special symmetry positions |
|
-Components
-THYROXINE-BINDING ... , 2 types, 2 molecules AB
#1: Protein | Mass: 39145.879 Da / Num. of mol.: 1 / Fragment: RESIDUES 32-380 / Mutation: YES Source method: isolated from a genetically manipulated source Details: RESIDUES 346-355 OF TBG WERE REPLACED BY GAMFLEAIPRS Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P05543 |
---|---|
#2: Protein/peptide | Mass: 4026.811 Da / Num. of mol.: 1 / Fragment: RESIDUES 381-415 Source method: isolated from a genetically manipulated source Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P05543 |
-Non-polymers , 4 types, 282 molecules
#3: Chemical | ChemComp-FUN / | ||||
---|---|---|---|---|---|
#4: Chemical | ChemComp-CA / #5: Chemical | ChemComp-EDO / #6: Water | ChemComp-HOH / | |
-Details
Compound details | ENGINEERED RESIDUE IN CHAIN A, ALA 366 TO GLY ENGINEERED RESIDUE IN CHAIN A, VAL 367 TO ALA ...ENGINEERED |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.35 Å3/Da / Density % sol: 48 % / Description: NONE |
---|---|
Crystal grow | pH: 5.4 / Details: 20% PEG3350, pH 5.4 |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.998 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.998 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→34.58 Å / Num. obs: 40382 / % possible obs: 92.6 % / Observed criterion σ(I): 2 / Redundancy: 3.7 % / Rmerge(I) obs: 0.19 / Net I/σ(I): 4.3 |
Reflection shell | Resolution: 1.7→1.79 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.55 / Mean I/σ(I) obs: 1.7 / % possible all: 71.1 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2RIV Resolution: 1.7→86.44 Å / Cor.coef. Fo:Fc: 0.94 / Cor.coef. Fo:Fc free: 0.928 / SU B: 5.181 / SU ML: 0.079 / Cross valid method: THROUGHOUT / ESU R: 0.127 / ESU R Free: 0.118 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 10.798 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.7→86.44 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
|