+Open data
-Basic information
Entry | Database: PDB / ID: 5k1n | ||||||
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Title | Human TTR altered by a rhenium tris-carbonyl Pyta-C12 derivative | ||||||
Components | Transthyretin | ||||||
Keywords | TRANSPORT PROTEIN / Large conformational change / Human TTR / potentiality for scavenging beta-Amyloid in Alzheimer disease | ||||||
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: 1.81 Å | ||||||
Authors | Stura, E.A. / Ciccone, L. / Shepard, W. | ||||||
Citation | Journal: J.Struct.Biol. / Year: 2016 Title: Human TTR conformation altered by rhenium tris-carbonyl derivatives. Authors: Ciccone, L. / Policar, C. / Stura, E.A. / Shepard, W. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5k1n.cif.gz | 118.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5k1n.ent.gz | 91.7 KB | Display | PDB format |
PDBx/mmJSON format | 5k1n.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/k1/5k1n ftp://data.pdbj.org/pub/pdb/validation_reports/k1/5k1n | HTTPS FTP |
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-Related structure data
Related structure data | 5k1jSC 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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1 |
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Unit cell |
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-Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 12961.511 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P02766 |
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-Non-polymers , 7 types, 163 molecules
#2: Chemical | #3: Chemical | ChemComp-PEG / | #4: Chemical | #5: Chemical | ChemComp-ACT / | #6: Chemical | ChemComp-DMS / | #7: Chemical | ChemComp-IMD / | #8: 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: 2.29 Å3/Da / Density % sol: 46.23 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6 Details: protein: 10 mg/ml Dialysed in 100 milli-M NaCl, 50 milli-M sodium acetate, pH 5.5 precipitant: 21% polyethylene glycol 4,000 (PEG4K), 0.14 M imidazole malate, pH 6.0 + 3.6% polyethylene ...Details: protein: 10 mg/ml Dialysed in 100 milli-M NaCl, 50 milli-M sodium acetate, pH 5.5 precipitant: 21% polyethylene glycol 4,000 (PEG4K), 0.14 M imidazole malate, pH 6.0 + 3.6% polyethylene glycol monomethyl ether (MPEG5K), 30 mM sodium acetate pH 5.5 cryosoak: 40% SM3 (25 % diethylene glycol + 25 % ethylene glycol + 25 % glycerol + 25 % 1,4-dioxane) 50% PEG 8K and 0.5 milli-M of rhenium tris-carbonyl Pyta-C12 derivative. PH range: 5.5-6.0 / Temp details: temperature controlled room |
-Data collection
Diffraction | Mean temperature: 100 K / Ambient temp details: cryonozzle |
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Diffraction source | Source: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 2 / Wavelength: 1.175919 Å |
Detector | Type: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Apr 22, 2016 / Details: mirrors |
Radiation | Monochromator: crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.175919 Å / Relative weight: 1 |
Reflection | Resolution: 1.81→50 Å / Num. obs: 41147 / % possible obs: 98.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 2.6 % / CC1/2: 0.998 / Rmerge(I) obs: 0.065 / Rsym value: 0.052 / Net I/σ(I): 12.31 |
Reflection shell | Resolution: 1.81→1.86 Å / Redundancy: 2.6 % / Rmerge(I) obs: 0.782 / Mean I/σ(I) obs: 1.69 / % possible all: 98.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5K1J Resolution: 1.81→41.065 Å / SU ML: 0.2 / Cross valid method: THROUGHOUT / σ(F): 1.26 / Phase error: 24.74
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.81→41.065 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Origin x: 43.2491 Å / Origin y: 28.2877 Å / Origin z: 17.264 Å
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Refinement TLS group | Selection details: all |