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Yorodumi- PDB-3cfn: Crystal structure of human transthyretin in complex with 1-anilin... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3cfn | ||||||
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Title | Crystal structure of human transthyretin in complex with 1-anilino-8-naphthalene sulfonate | ||||||
Components | Transthyretin | ||||||
Keywords | TRANSPORT PROTEIN / human transthyretin / amyloid / familial amyloid polyneurophaty / 1 / 8-2AN / Disease mutation / Glycoprotein / Hormone / Polyneuropathy / Retinol-binding / Secreted / Thyroid hormone / Transport / Vitamin A | ||||||
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 / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.87 Å | ||||||
Authors | Lima, L.-M.T.R. / Foguel, D. / Polikarpov, I. | ||||||
Citation | Journal: Bioorg.Med.Chem. / Year: 2010 Title: Identification of a novel ligand binding motif in the transthyretin channel. Authors: Lima, L.M. / Silva, V.D. / Palmieri, L.D. / Oliveira, M.C. / Foguel, D. / Polikarpov, I. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3cfn.cif.gz | 65.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3cfn.ent.gz | 47.9 KB | Display | PDB format |
PDBx/mmJSON format | 3cfn.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3cfn_validation.pdf.gz | 1.1 MB | Display | wwPDB validaton report |
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Full document | 3cfn_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 3cfn_validation.xml.gz | 14.4 KB | Display | |
Data in CIF | 3cfn_validation.cif.gz | 19.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/cf/3cfn ftp://data.pdbj.org/pub/pdb/validation_reports/cf/3cfn | HTTPS FTP |
-Related structure data
Related structure data | 3cfmSC 3cfqC 3cftC 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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2 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: CYS / Beg label comp-ID: CYS / End auth comp-ID: ALA / End label comp-ID: ALA / Refine code: 5 / Auth seq-ID: 10 - 120 / Label seq-ID: 1 - 111
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-Components
#1: Protein | Mass: 12961.511 Da / Num. of mol.: 2 / Fragment: UNP residue 30-147 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: TTR, PALB / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / 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: 2.36 Å3/Da / Density % sol: 47.81 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: mother liquor: 100 mM Tris, pH 7.5, 100 mM KCl, 20 % v/v PEG 400; drop consisting of 1 uL mother liquor and 1 uL wtTTR 10 mg/mL; crystals appeared in about 5 days; complex obtained by ...Details: mother liquor: 100 mM Tris, pH 7.5, 100 mM KCl, 20 % v/v PEG 400; drop consisting of 1 uL mother liquor and 1 uL wtTTR 10 mg/mL; crystals appeared in about 5 days; complex obtained by soaking in mother liquor supplemented with saturating amount of ligand., VAPOR DIFFUSION, HANGING DROP, temperature 291K |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU ULTRAX 18 / Wavelength: 1.5418 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Jun 1, 2005 / Details: Osmic | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.87→51.168 Å / Num. all: 19713 / Num. obs: 19329 / % possible obs: 93.5 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 7.2 % / Biso Wilson estimate: 17.7 Å2 / Rmerge(I) obs: 0.043 / Rsym value: 0.043 / Net I/σ(I): 13 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Phasing
Phasing | Method: molecular replacement | |||||||||
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Phasing MR | Rfactor: 0.587 / Cor.coef. Fo:Fc: 0.33
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3CFM Resolution: 1.87→26.25 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.922 / SU B: 3.122 / SU ML: 0.097 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.18 / ESU R Free: 0.162 / 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: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 17.107 Å2
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Refine analyze | Luzzati coordinate error obs: 0.064 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.87→26.25 Å
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Refine LS restraints |
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Refine LS restraints NCS | Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION
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LS refinement shell | Resolution: 1.87→1.918 Å / Total num. of bins used: 20
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