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Yorodumi- PDB-2trh: TERTIARY STRUCTURES OF THREE AMYLOIDOGENIC TRANSTHYRETIN VARIANTS... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2trh | ||||||
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Title | TERTIARY STRUCTURES OF THREE AMYLOIDOGENIC TRANSTHYRETIN VARIANTS AND IMPLICATIONS FOR AMYLOID FIBRIL FORMATION | ||||||
Components | TRANSTHYRETIN | ||||||
Keywords | TRANSPORT / ALBUMIN / RETINOL-BINDING / VITAMIN A / AMYLOID / THYROID HORMONE / LIVER / PLASMA / CEREBROSPINAL FLUID / POLYNEUROPATHY / DISEASE MUTATION / THYROXINE / PREALBUMIN | ||||||
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 / Resolution: 1.9 Å | ||||||
Authors | Schormann, N. / Murrell, J.R. / Benson, M.D. | ||||||
Citation | Journal: Amyloid / Year: 1998 Title: Tertiary structures of amyloidogenic and non-amyloidogenic transthyretin variants: new model for amyloid fibril formation. Authors: Schormann, N. / Murrell, J.R. / Benson, M.D. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2trh.cif.gz | 59.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2trh.ent.gz | 45.1 KB | Display | PDB format |
PDBx/mmJSON format | 2trh.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2trh_validation.pdf.gz | 419.6 KB | Display | wwPDB validaton report |
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Full document | 2trh_full_validation.pdf.gz | 426.1 KB | Display | |
Data in XML | 2trh_validation.xml.gz | 12.7 KB | Display | |
Data in CIF | 2trh_validation.cif.gz | 16.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/tr/2trh ftp://data.pdbj.org/pub/pdb/validation_reports/tr/2trh | HTTPS FTP |
-Related structure data
Related structure data | 1b0wC 1bzdC 1bzeC 1tshC 2tryC 1ttaS 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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Noncrystallographic symmetry (NCS) | NCS oper: (Code: given Matrix: (-0.99002, 0.14091, -0.00197), Vector: |
-Components
#1: Protein | Mass: 13831.412 Da / Num. of mol.: 2 / Mutation: VARIANT R10C Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Cell line: HB101 / Plasmid: PCZ11 / Cell line (production host): HB101 / Production host: Escherichia coli (E. coli) / References: UniProt: P02766 #2: 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: 2.2 Å3/Da / Density % sol: 52.2 % |
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Crystal grow | pH: 6.5 Details: PURIFIED PROTEIN (20MG/ML IN 100MM TRIS BUFFER, PH 7.5) WAS CRYSTALLIZED FROM\\ 2.25M AMMONIUM SULFATE, 100MM CITRATE BUFFER, PH 5.5 AT ROOM TEMPERATURE.\\, pH 6.5 PH range: 5.5-7.5 / Temp details: room temp |
-Data collection
Diffraction | Mean temperature: 296 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RUH2R / Wavelength: 1.5418 |
Detector | Type: RIGAKU RAXIS IIC / Detector: IMAGE PLATE / Date: Jun 1, 1995 / Details: COLLIMATOR |
Radiation | Monochromator: GRAPHITE(002) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→52.22 Å / Num. obs: 20855 / % possible obs: 88.6 % / Observed criterion σ(I): 1 / Redundancy: 4.3 % / Biso Wilson estimate: 11.6 Å2 / Rmerge(I) obs: 0.109 / Rsym value: 0.073 / Net I/σ(I): 5 |
Reflection shell | Resolution: 1.8→1.86 Å / Redundancy: 2 % / Rmerge(I) obs: 0.27 / Mean I/σ(I) obs: 1.9 / Rsym value: 0.22 / % possible all: 74.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1TTA Resolution: 1.9→5 Å / Rfactor Rfree error: 0.009 / Cross valid method: THROUGHOUT / σ(F): 2 Details: RESIDUES IN REGIONS WITH LOW ELECTRON DENSITY (RESIDUES 1 - 9 AT N-TERMINUS AND RESIDUES 124 - 127 AT C-TERMINUS) WERE REFINED WITH OCCUPANCIES SET TO 0.5.
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Displacement parameters | Biso mean: 22.6 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze | Luzzati coordinate error obs: 0.25 Å / Luzzati d res low obs: 5 Å / Luzzati sigma a obs: 0.34 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.9→5 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.9→1.98 Å / Rfactor Rfree error: 0.04
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Xplor file |
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