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Yorodumi- PDB-2riw: The Reactive loop cleaved human Thyroxine Binding Globulin comple... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2riw | |||||||||
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Title | The Reactive loop cleaved human Thyroxine Binding Globulin complexed with thyroxine | |||||||||
Components | (Thyroxine-binding globulin) x 2 | |||||||||
Keywords | SIGNALING PROTEIN / Thyroxine binding globulin / thyroxine / complex / serpin / TBG / Disease mutation / Glycoprotein / Secreted | |||||||||
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: 2.04 Å | |||||||||
Authors | Zhou, A. / Wei, Z. / Stanley, P.L.D. / Read, R.J. / Stein, P.E. / Carrell, R.W. | |||||||||
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 | 2riw.cif.gz | 95.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2riw.ent.gz | 70.5 KB | Display | PDB format |
PDBx/mmJSON format | 2riw.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2riw_validation.pdf.gz | 943.6 KB | Display | wwPDB validaton report |
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Full document | 2riw_full_validation.pdf.gz | 946.2 KB | Display | |
Data in XML | 2riw_validation.xml.gz | 18.5 KB | Display | |
Data in CIF | 2riw_validation.cif.gz | 27.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ri/2riw ftp://data.pdbj.org/pub/pdb/validation_reports/ri/2riw | HTTPS FTP |
-Related structure data
Related structure data | 2rivSC 2xn3C 2xn5C 2xn6C 2xn7C 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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3 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 37887.547 Da / Num. of mol.: 1 / Fragment: N-terminal domain, UNP residues 39-375 Source method: isolated from a genetically manipulated source Details: Purified from the supernatant of the cell lysate / Source: (gene. exp.) Homo sapiens (human) / Gene: SERPINA7, TBG / Plasmid: pET16b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21Star (DE3) / References: UniProt: P05543 |
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#2: Protein/peptide | Mass: 4605.383 Da / Num. of mol.: 1 Fragment: reactive loop cleaved TBG, C-teemingly domain, UNP residues 376-415 Source method: isolated from a genetically manipulated source Details: Purified from the supernatant of the cell lysate / Source: (gene. exp.) Homo sapiens (human) / Gene: SERPINA7, TBG / Plasmid: pET16b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21Star (DE3) / References: UniProt: P05543 |
#3: Chemical | ChemComp-T44 / |
#4: Water | ChemComp-HOH / |
Sequence details | THE REACTIVE LOOP P10-P1' CLEAVED CONFORMATION OF TBG WAS MUTATED TO GAMFLEAIPRS. THE FIRST ...THE REACTIVE LOOP P10-P1' CLEAVED CONFORMATI |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.41 Å3/Da / Density % sol: 48.98 % |
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Crystal grow | Temperature: 298 K / Method: evaporation / pH: 7.4 Details: 20% PEG 3350, 0.2M CaCl2, pH 7.4, EVAPORATION, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SRS / Beamline: PX14.1 / Wavelength: 1.5419 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: May 22, 2007 / Details: mirrors |
Radiation | Monochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5419 Å / Relative weight: 1 |
Reflection | Resolution: 2.04→24.8 Å / Num. all: 25769 / Num. obs: 25486 / % possible obs: 98.9 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 3.3 % / Rmerge(I) obs: 0.056 / Net I/σ(I): 14.1 |
Reflection shell | Resolution: 2.04→2.09 Å / Rmerge(I) obs: 0.168 / Mean I/σ(I) obs: 4.2 / Num. unique all: 1692 / % possible all: 91 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2RIV Resolution: 2.04→23.11 Å / Cor.coef. Fo:Fc: 0.935 / Cor.coef. Fo:Fc free: 0.9 / SU B: 6.589 / SU ML: 0.113 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 2 / σ(I): 4.2 / ESU R: 0.21 / ESU R Free: 0.182 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 21.142 Å2
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Refinement step | Cycle: LAST / Resolution: 2.04→23.11 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.038→2.091 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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