+Open data
-Basic information
Entry | Database: PDB / ID: 1sn2 | ||||||
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Title | Crystal Structure of Sea Bream Transthyretin at 1.90A Resolution | ||||||
Components | transthyretin | ||||||
Keywords | TRANSPORT PROTEIN | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Sparus aurata (gilthead seabream) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 Å | ||||||
Authors | Eneqvist, T. / Lundberg, E. / Karlsson, A. / Huang, S. / Cantos, C.R. / Power, D.M. / Sauer-Eriksson, A.E. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2004 Title: High resolution crystal structures of piscine transthyretin reveal different binding modes for triiodothyronine and thyroxine. Authors: Eneqvist, T. / Lundberg, E. / Karlsson, A. / Huang, S. / Santos, C.R. / Power, D.M. / Sauer-Eriksson, A.E. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1sn2.cif.gz | 107.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1sn2.ent.gz | 82.8 KB | Display | PDB format |
PDBx/mmJSON format | 1sn2.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/sn/1sn2 ftp://data.pdbj.org/pub/pdb/validation_reports/sn/1sn2 | HTTPS FTP |
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-Related structure data
Related structure data | 1sn0C 1sn5C 1f41S 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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Details | One asymmetric unit contains one transthyretin homo-tetramer |
-Components
#1: Protein | Mass: 14027.579 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Sparus aurata (gilthead seabream) / Production host: Escherichia coli (E. coli) / References: UniProt: Q9PTT3 #2: Chemical | ChemComp-SO4 / | #3: 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: 2.14 Å3/Da / Density % sol: 42.64 % |
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Crystal grow | Temperature: 296 K / Method: vapor diffusion, hanging drop / pH: 5 Details: PEG 1550 MME, sodium citrate, ammonium sulphate, nickel sulphate, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 296K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X11 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Relative weight: 1 |
Reflection | Resolution: 1.75→50 Å / Num. obs: 46104 / % possible obs: 97.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Rmerge(I) obs: 0.047 |
Reflection shell | Resolution: 1.75→1.81 Å / Rmerge(I) obs: 0.451 / % possible all: 92.2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: Human transthyretin, pdb code 1F41 Resolution: 1.75→19.84 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.957 / SU B: 3.603 / SU ML: 0.116 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.128 / ESU R Free: 0.119 / Stereochemistry target values: MAXIMUM LIKELIHOOD / 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: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 21.58 Å2
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Refinement step | Cycle: LAST / Resolution: 1.75→19.84 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.751→1.796 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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