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Yorodumi- PDB-5zfx: Crystal Structure of Triosephosphate isomerase from Opisthorchis ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5zfx | ||||||
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Title | Crystal Structure of Triosephosphate isomerase from Opisthorchis viverrini | ||||||
Components | Triosephosphate isomerase | ||||||
Keywords | ISOMERASE / Tim-barrel / Triosephosphate isomerase | ||||||
Function / homology | Function and homology information triose-phosphate isomerase / triose-phosphate isomerase activity / gluconeogenesis / glycolytic process Similarity search - Function | ||||||
Biological species | Opisthorchis viverrini (Southeast Asian liver fluke) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.751 Å | ||||||
Authors | Son, J. / Kim, S. / Kim, S.E. / Lee, H. / Lee, M.R. / Hwang, K.Y. | ||||||
Citation | Journal: Sci Rep / Year: 2018 Title: Structural Analysis of an Epitope Candidate of Triosephosphate Isomerase in Opisthorchis viverrini. Authors: Son, J. / Kim, S. / Kim, S.E. / Lee, H. / Lee, M.R. / Hwang, K.Y. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5zfx.cif.gz | 228.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5zfx.ent.gz | 179.4 KB | Display | PDB format |
PDBx/mmJSON format | 5zfx.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zf/5zfx ftp://data.pdbj.org/pub/pdb/validation_reports/zf/5zfx | HTTPS FTP |
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-Related structure data
Related structure data | 5zg4C 5zg5C 5zgaC 1tphS 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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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Ens-ID: 1 / End auth comp-ID: ALA / End label comp-ID: ALA
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-Components
#1: Protein | Mass: 30008.338 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Opisthorchis viverrini (Southeast Asian liver fluke) Gene: T265_10017 / Plasmid: pET17b / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: A0A074Z863, triose-phosphate isomerase #2: Chemical | #3: Water | ChemComp-HOH / | Sequence details | The sequence conflicts may be resulted from the difference of subspecies of the source organism. | |
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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: 2.22 Å3/Da / Density % sol: 39.6 % / Mosaicity: 0.508 ° |
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Crystal grow | Temperature: 293 K / Method: evaporation / pH: 8.5 / Details: PEG 3350 |
-Data collection
Diffraction | Mean temperature: 273 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: PAL/PLS / Beamline: 5C (4A) / Wavelength: 1.00001 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 6, 2013 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1.00001 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.75→50 Å / Num. obs: 96825 / % possible obs: 98.8 % / Redundancy: 5.6 % / Biso Wilson estimate: 15.65 Å2 / Rmerge(I) obs: 0.105 / Χ2: 11.73 / Net I/σ(I): 37.7 / Num. measured all: 541897 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1TPH Resolution: 1.751→44.075 Å / SU ML: 0.16 / Cross valid method: THROUGHOUT / σ(F): 1.56 / Phase error: 18.42 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 87.76 Å2 / Biso mean: 21.1921 Å2 / Biso min: 5.06 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.751→44.075 Å
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Refine LS restraints |
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Refine LS restraints NCS |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14
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