+Open data
-Basic information
Entry | Database: PDB / ID: 1bz8 | ||||||
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Title | TRANSTHYRETIN (DEL VAL122) | ||||||
Components | PROTEIN (TRANSTHYRETIN) | ||||||
Keywords | SIGNALING PROTEIN / THYROID HORMONE / LIVER / PLASMA / CEREBROSPINAL FLUID / POLYNEUROPATHY / DISEASE MUTATION / DELETION MUTANT / TRANSPORT / THYROXINE | ||||||
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: 2 Å | ||||||
Authors | Schormann, N. / Uemichi, T. / Benson, M.D. | ||||||
Citation | Journal: To be Published Title: Structural Analysis of Delval122 Transthyretin-A Deletion Mutant Authors: Schormann, N. / Uemichi, T. / 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 | 1bz8.cif.gz | 59.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1bz8.ent.gz | 44.3 KB | Display | PDB format |
PDBx/mmJSON format | 1bz8.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1bz8_validation.pdf.gz | 423.8 KB | Display | wwPDB validaton report |
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Full document | 1bz8_full_validation.pdf.gz | 433.1 KB | Display | |
Data in XML | 1bz8_validation.xml.gz | 12.6 KB | Display | |
Data in CIF | 1bz8_validation.cif.gz | 16 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bz/1bz8 ftp://data.pdbj.org/pub/pdb/validation_reports/bz/1bz8 | HTTPS FTP |
-Related structure data
Related structure data | 1tshS 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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Noncrystallographic symmetry (NCS) | NCS oper: (Code: given Matrix: (-0.9919, 0.12697, -0.00413), Vector: |
-Components
#1: Protein | Mass: 13678.229 Da / Num. of mol.: 2 / Mutation: TRINUCLEOTIDE DELETION VARIANT DELVAL122 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) Description: VARIANT WAS PRODUCED BY SITE DIRECTED MUTAGENESIS USING A MISMATCH PRIMER AND THE NORMAL R-TTR/ PCZ11 CONSTRUCT 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: 2.3 Å3/Da / Density % sol: 44.92 % Description: AFTER INITIAL REFINEMENT THE C-TERMINAL RESIDUES WERE REBUILT USING AN OMIT MAP, SINCE THE DELETION RESULTS IN A REMOVAL OF VALINE AT POSITION 122 |
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Crystal grow | pH: 6.5 / Details: pH 6.50 |
-Data collection
Diffraction | Mean temperature: 296 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 |
Detector | Type: RIGAKU RAXIS IIC / Detector: IMAGE PLATE / Date: Jul 1, 1996 / Details: COLLIMATOR |
Radiation | Monochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→65.1 Å / Num. obs: 17380 / % possible obs: 74 % / Observed criterion σ(I): 1 / Redundancy: 2.7 % / Biso Wilson estimate: 19.2 Å2 / Rmerge(I) obs: 0.082 / Rsym value: 0.052 / Net I/σ(I): 6.5 |
Reflection shell | Resolution: 1.8→1.92 Å / Redundancy: 1.9 % / Rmerge(I) obs: 0.23 / Mean I/σ(I) obs: 1.7 / Rsym value: 0.22 / % possible all: 56.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1TSH Resolution: 2→6 Å / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2 Details: RESIDUES IN REGIONS WITH LOW ELECTRON DENSITY (RESIDUES 1 - 9 AT N-TERMINUS AND RESIDUES 122 - 126 AT C-TERMINUS) WERE REFINED WITH OCCUPANCIES SET TO 0.5.
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Displacement parameters | Biso mean: 28.6 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze | Luzzati coordinate error obs: 0.26 Å / Luzzati d res low obs: 6 Å / Luzzati sigma a obs: 0.3 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2→6 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2→2.09 Å / Total num. of bins used: 8
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Xplor file |
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