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Yorodumi- PDB-4l1s: Covalent modification of transthyretin K15 by yielding the fluore... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4l1s | ||||||
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Title | Covalent modification of transthyretin K15 by yielding the fluorescent conjugate (E)-3-(dimethylamino)-5-(4-hydroxy-3,5-dimethylstyryl)benzamide | ||||||
Components | Transthyretin | ||||||
Keywords | TRANSPORT PROTEIN / Hormone transport protein / Thyroxine / retinol | ||||||
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: 1.5 Å | ||||||
Authors | Connelly, S. / Wilson, I.A. | ||||||
Citation | Journal: Biopolymers / Year: 2014 Title: Fluorogenic small molecules requiring reaction with a specific protein to create a fluorescent conjugate for biological imaging-what we know and what we need to learn. Authors: Baranczak, A. / Connelly, S. / Liu, Y. / Choi, S. / Grimster, N.P. / Powers, E.T. / Wilson, I.A. / Kelly, J.W. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4l1s.cif.gz | 116.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4l1s.ent.gz | 90.8 KB | Display | PDB format |
PDBx/mmJSON format | 4l1s.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4l1s_validation.pdf.gz | 1 MB | Display | wwPDB validaton report |
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Full document | 4l1s_full_validation.pdf.gz | 1 MB | Display | |
Data in XML | 4l1s_validation.xml.gz | 13.6 KB | Display | |
Data in CIF | 4l1s_validation.cif.gz | 18.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/l1/4l1s ftp://data.pdbj.org/pub/pdb/validation_reports/l1/4l1s | HTTPS FTP |
-Related structure data
Related structure data | 4l1tC 2fbrS 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 on special symmetry positions |
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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 / Plasmid: pmmHA / Production host: Escherichia coli (E. coli) / Strain (production host): Epicurian Gold / References: UniProt: P02766 #2: Chemical | #3: Water | ChemComp-HOH / | Nonpolymer details | UPON INCUBATION OF 1W4 WITH THE PROTEIN TRANSTHYRETIN THE MOLECULE CHEMOSELECTIVELY REACTS WITH K15 ...UPON INCUBATION | |
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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: 2.04 Å3/Da / Density % sol: 39.75 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 5.5 Details: The wt-TTR was concentrated to 4 mg/ml in 10 mM NaPi, 100 mM KCl, at pH 7.6 and co-crystallized at room temperature with inhibitors using the vapor-diffusion sitting drop method, crystals ...Details: The wt-TTR was concentrated to 4 mg/ml in 10 mM NaPi, 100 mM KCl, at pH 7.6 and co-crystallized at room temperature with inhibitors using the vapor-diffusion sitting drop method, crystals were grown from 1.395 M sodium citrate, 3.5% v/v glycerol at ph 5.5. The crystals were frozen using a cryo-protectant solution of 1.395 m sodium citrate, ph 5.5, containing 10% v/v glycerol, vapor diffusion, sitting drop, temperature 298.0, VAPOR DIFFUSION, SITTING DROP |
-Data collection
Diffraction | Mean temperature: 200 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.9797 Å |
Detector | Type: PSI PILATUS 6M / Detector: PIXEL / Date: Aug 2, 2012 Details: SINGLE CRYSTAL SI(111) BENT MONOCHROMATOR (HORIZONTAL FOCUSING) |
Radiation | Monochromator: ASYMMETRIC CUT 4.965 DEGS SIDE SCATTERING BENT CUBE-ROOT I -BEAM SINGLE CRYSTAL Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9797 Å / Relative weight: 1 |
Reflection | Resolution: 1.5→37.48 Å / Num. obs: 36103 / % possible obs: 98.5 % / Redundancy: 6.1 % / Biso Wilson estimate: 12.6 Å2 / Rsym value: 0.059 / Net I/σ(I): 18.6 |
Reflection shell | Resolution: 1.5→1.58 Å / Redundancy: 5.9 % / Mean I/σ(I) obs: 5.9 / Num. unique all: 5007 / Rsym value: 0.537 / % possible all: 95.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2FBR Resolution: 1.5→37.48 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.967 / WRfactor Rfree: 0.1991 / WRfactor Rwork: 0.1657 / Occupancy max: 1 / Occupancy min: 0.12 / FOM work R set: 0.8823 / SU R Cruickshank DPI: 0.091 / SU Rfree: 0.0705 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.091 / ESU R Free: 0.071 / 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: 97.86 Å2 / Biso mean: 24.9124 Å2 / Biso min: 5.2 Å2
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Refinement step | Cycle: LAST / Resolution: 1.5→37.48 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.502→1.541 Å / Total num. of bins used: 20
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