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Yorodumi- PDB-4mas: High Resolution Structure of Wild Type Human Transthyretin in Com... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4mas | ||||||
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Title | High Resolution Structure of Wild Type Human Transthyretin in Complex with 3,3',5,5'-tetrachloro-[1,1'-biphenyl]-4,4'diol | ||||||
Components | Transthyretin | ||||||
Keywords | TRANSPORT PROTEIN/INHIBITOR / hormone / binding protein / hormone transport / thyroxine / retinol binding protein / TRANSPORT PROTEIN-INHIBITOR complex | ||||||
Function / homology | Function and homology information Retinoid cycle disease events / The canonical retinoid cycle in rods (twilight vision) / thyroid hormone binding / purine nucleobase metabolic process / Non-integrin membrane-ECM interactions / Retinoid metabolism and transport / hormone activity / azurophil granule lumen / Amyloid fiber formation / Neutrophil degranulation ...Retinoid cycle disease events / The canonical retinoid cycle in rods (twilight vision) / thyroid hormone binding / purine nucleobase metabolic process / Non-integrin membrane-ECM interactions / Retinoid metabolism and transport / hormone activity / azurophil granule lumen / Amyloid fiber formation / Neutrophil degranulation / extracellular space / extracellular exosome / extracellular region / identical protein binding Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.22 Å | ||||||
Authors | Connelly, S. / Bradbury, N.C. / Wilson, I.A. | ||||||
Citation | Journal: To be Published Title: High Resolution Structure of Wild Type Human Transthyretin in Complex with 3,3',5,5'-tetrachloro-[1,1'-biphenyl]-4,4'diol Authors: Connelly, S. / Bradbury, N.C. / Wilson, I.A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4mas.cif.gz | 117.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4mas.ent.gz | 91.9 KB | Display | PDB format |
PDBx/mmJSON format | 4mas.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4mas_validation.pdf.gz | 1.1 MB | Display | wwPDB validaton report |
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Full document | 4mas_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 4mas_validation.xml.gz | 13.6 KB | Display | |
Data in CIF | 4mas_validation.cif.gz | 19.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ma/4mas ftp://data.pdbj.org/pub/pdb/validation_reports/ma/4mas | HTTPS FTP |
-Related structure data
Related structure data | 2fbrS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 13777.360 Da / Num. of mol.: 2 / Fragment: UNP residues 21-147 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: PALB, TTR / Plasmid: pmmHA / Production host: Escherichia coli (E. coli) / Strain (production host): Epicurean Gold / References: UniProt: P02766 #2: Chemical | #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: 2.15 Å3/Da / Density % sol: 42.92 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 5.5 Details: 4 mg/ML wt-TTR in 10 mM sodium phosphate, 100 mM potassium chloride, pH 7.6, co-crystallized with inhibitor, crystallization solution: 1.395 M sodium citrate, 3.5% v/v glycerol, pH 5.5, ...Details: 4 mg/ML wt-TTR in 10 mM sodium phosphate, 100 mM potassium chloride, pH 7.6, co-crystallized with inhibitor, crystallization solution: 1.395 M sodium citrate, 3.5% v/v glycerol, pH 5.5, cryoprotectant: 1.395 M sodium citrate, pH 5.5, 10% v/v glycerol, VAPOR DIFFUSION, SITTING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 200 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.9797 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 27, 2013 / Details: Rh coated flat mirror |
Radiation | Monochromator: Side scattering bent cube-root I-beam single crystal, asymmetric cut 4.965 degrees Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9797 Å / Relative weight: 1 |
Reflection | Resolution: 1.22→35.873 Å / Num. obs: 70897 / % possible obs: 99.5 % / Redundancy: 6.3 % / Biso Wilson estimate: 13.9 Å2 / Rsym value: 0.028 / Net I/σ(I): 27.6 |
Reflection shell | Resolution: 1.22→1.29 Å / Redundancy: 6 % / Mean I/σ(I) obs: 3.5 / Num. unique all: 10085 / Rsym value: 0.515 / % possible all: 98.2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2FBR Resolution: 1.22→35.873 Å / Cor.coef. Fo:Fc: 0.976 / Cor.coef. Fo:Fc free: 0.972 / SU B: 1.038 / SU ML: 0.021 / Cross valid method: THROUGHOUT / ESU R: 0.04 / ESU R Free: 0.039 / 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: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 17.368 Å2
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Refinement step | Cycle: LAST / Resolution: 1.22→35.873 Å
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Refine LS restraints |
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