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Yorodumi- PDB-4ikk: Crystal structure of wild-type human transthyretin in complex wit... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4ikk | ||||||
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Title | Crystal structure of wild-type human transthyretin in complex with sulindac | ||||||
Components | Transthyretin | ||||||
Keywords | TRANSPORT PROTEIN / Hormone carrier / Retinol binding protein | ||||||
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 / molecular replacement / Resolution: 1.9 Å | ||||||
Authors | Lima, L.M.T.R. | ||||||
Citation | Journal: To be Published Title: Crystal structure of wild-type human transthyretin in complex with sulindac Authors: Lima, L.M.T.R. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4ikk.cif.gz | 64.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4ikk.ent.gz | 48.1 KB | Display | PDB format |
PDBx/mmJSON format | 4ikk.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4ikk_validation.pdf.gz | 988.9 KB | Display | wwPDB validaton report |
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Full document | 4ikk_full_validation.pdf.gz | 999.8 KB | Display | |
Data in XML | 4ikk_validation.xml.gz | 15.4 KB | Display | |
Data in CIF | 4ikk_validation.cif.gz | 20.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ik/4ikk ftp://data.pdbj.org/pub/pdb/validation_reports/ik/4ikk | HTTPS FTP |
-Related 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: 13777.360 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: TTR, PALB / Production host: Escherichia coli (E. coli) / 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: 1.99 Å3/Da / Density % sol: 38.34 % / Mosaicity: 0.992 ° |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 10mg/mL wtTTR, 0.2M Calcium chloride, 0.1M HEPES sodium pH 7.5, 28% v/v Polyethylene glycol 400 (Hampton Research's Crystal Screen I, #14), VAPOR DIFFUSION, HANGING DROP, temperature 291K |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: LNLS / Beamline: D03B-MX1 / Wavelength: 1.425 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: MAR CCD 165 mm / Detector: CCD / Date: Sep 16, 2008 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1.425 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.9→83.13 Å / Num. all: 17616 / Num. obs: 17616 / % possible obs: 98.1 % / Redundancy: 3.3 % / Rmerge(I) obs: 0.075 / Rsym value: 0.075 / Net I/σ(I): 12.2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Phasing
Phasing | Method: molecular replacement | |||||||||
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Phasing MR |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.9→19.76 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.925 / WRfactor Rfree: 0.2298 / WRfactor Rwork: 0.1837 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.8396 / SU B: 4.194 / SU ML: 0.121 / SU R Cruickshank DPI: 0.2032 / SU Rfree: 0.176 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.203 / ESU R Free: 0.176 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES: REFINED INDIVIDUALLY
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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 max: 55.48 Å2 / Biso mean: 25.5027 Å2 / Biso min: 10.36 Å2
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Refinement step | Cycle: LAST / Resolution: 1.9→19.76 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.9→1.949 Å / Total num. of bins used: 20
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