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Yorodumi- PDB-5dwp: Crystal Structure of human transthyretin (TTR) processed with the... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5dwp | ||||||
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Title | Crystal Structure of human transthyretin (TTR) processed with the CrystalDirect automated mounting and cryo-cooling technology | ||||||
Components | Transthyretin | ||||||
Keywords | TRANSFERASE / transthyretin | ||||||
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: 1.2 Å | ||||||
Authors | Zander, U. / Cornaciu, I. / Forsyth, T. / Yee, A. / Marquez, J.A. | ||||||
Citation | Journal: Acta Crystallogr D Struct Biol / Year: 2016 Title: Automated harvesting and processing of protein crystals through laser photoablation. Authors: Zander, U. / Hoffmann, G. / Cornaciu, I. / Marquette, J.P. / Papp, G. / Landret, C. / Seroul, G. / Sinoir, J. / Rower, M. / Felisaz, F. / Rodriguez-Puente, S. / Mariaule, V. / Murphy, P. / ...Authors: Zander, U. / Hoffmann, G. / Cornaciu, I. / Marquette, J.P. / Papp, G. / Landret, C. / Seroul, G. / Sinoir, J. / Rower, M. / Felisaz, F. / Rodriguez-Puente, S. / Mariaule, V. / Murphy, P. / Mathieu, M. / Cipriani, F. / Marquez, J.A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5dwp.cif.gz | 114.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5dwp.ent.gz | 88.6 KB | Display | PDB format |
PDBx/mmJSON format | 5dwp.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dw/5dwp ftp://data.pdbj.org/pub/pdb/validation_reports/dw/5dwp | HTTPS FTP |
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-Related structure data
Related structure data | 5amwC 5amxC 5amzC 5an4C 5andC 5aneC 5angC 5aniC 5anjC 5ankC 5anlC 5anoC 5ebhC 4pvlS 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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Unit cell |
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Components on special symmetry positions |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Ens-ID: 1 / Refine code: 6
NCS oper:
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-Components
#1: Protein | Mass: 12703.217 Da / Num. of mol.: 2 / Fragment: UNP residues 31-145 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: TTR, PALB Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria) References: UniProt: P02766 #2: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.17 Å3/Da / Density % sol: 43.4 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop Details: 0.1 M sodium citrate, 1.6 M ammonium sulfate, pH=5.0 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 0.9765 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 25, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9765 Å / Relative weight: 1 |
Reflection | Resolution: 1.2→19.63 Å / Num. obs: 69740 / % possible obs: 97 % / Redundancy: 4.5 % / Rmerge(I) obs: 0.068 / Net I/σ(I): 8.2 |
Reflection shell | Resolution: 1.2→1.26 Å |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4PVL Resolution: 1.2→19.63 Å / Cor.coef. Fo:Fc: 0.975 / Cor.coef. Fo:Fc free: 0.965 / SU B: 2.017 / SU ML: 0.038 / Cross valid method: THROUGHOUT / ESU R: 0.043 / ESU R Free: 0.043 / 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: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 17.953 Å2
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Refinement step | Cycle: LAST / Resolution: 1.2→19.63 Å
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Refine LS restraints |
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