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Yorodumi- PDB-2xn3: Crystal structure of thyroxine-binding globulin complexed with me... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2xn3 | ||||||
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Title | Crystal structure of thyroxine-binding globulin complexed with mefenamic acid | ||||||
Components | (THYROXINE-BINDING GLOBULIN) 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 / MOLECULAR REPLACEMENT / Resolution: 2.09 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 |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2xn3.cif.gz | 161.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2xn3.ent.gz | 127.1 KB | Display | PDB format |
PDBx/mmJSON format | 2xn3.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2xn3_validation.pdf.gz | 455.9 KB | Display | wwPDB validaton report |
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Full document | 2xn3_full_validation.pdf.gz | 460 KB | Display | |
Data in XML | 2xn3_validation.xml.gz | 16.8 KB | Display | |
Data in CIF | 2xn3_validation.cif.gz | 23.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xn/2xn3 ftp://data.pdbj.org/pub/pdb/validation_reports/xn/2xn3 | HTTPS FTP |
-Related structure data
Related structure data | 2rivSC 2riwC 2xn5C 2xn6C 2xn7C C: citing same article (ref.) 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: Protein | Mass: 38399.074 Da / Num. of mol.: 1 / Fragment: RESIDUES 33-375 / 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 |
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#2: Protein/peptide | Mass: 4605.383 Da / Num. of mol.: 1 / Fragment: RESIDUES 377-415 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 |
#3: Chemical | ChemComp-ID8 / |
#4: Water | ChemComp-HOH / |
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 |
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-Sample preparation
Crystal | Density Matthews: 2.35 Å3/Da / Density % sol: 48 % / Description: NONE |
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Crystal grow | pH: 5.4 / Details: 20% PEG3350, PH 5.4 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 |
Detector | Date: Oct 11, 2007 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.09→21.97 Å / Num. obs: 24692 / % possible obs: 98.2 % / Observed criterion σ(I): 2 / Redundancy: 5.2 % / Rmerge(I) obs: 0.09 / Net I/σ(I): 14.5 |
Reflection shell | Resolution: 2.09→2.21 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.32 / Mean I/σ(I) obs: 3.3 / % possible all: 88.5 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2RIV Resolution: 2.09→86.39 Å / Cor.coef. Fo:Fc: 0.94 / Cor.coef. Fo:Fc free: 0.913 / SU B: 11.626 / SU ML: 0.139 / Cross valid method: THROUGHOUT / ESU R: 0.238 / ESU R Free: 0.201 / Stereochemistry target values: MAXIMUM LIKELIHOOD PDB / 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: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 32.786 Å2
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Refinement step | Cycle: LAST / Resolution: 2.09→86.39 Å
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Refine LS restraints |
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