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Yorodumi- PDB-6nxx: Crystal structure of Arabidopsis thaliana cytosolic triosephospha... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6nxx | ||||||
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Title | Crystal structure of Arabidopsis thaliana cytosolic triosephosphate isomerase C218K mutant | ||||||
Components | Triosephosphate isomerase, cytosolic | ||||||
Keywords | ISOMERASE / Triosephosphate isomerase Crystal structure mutant dimer redox regulation | ||||||
Function / homology | Function and homology information plant-type cell wall / plasmodesma / apoplast / plant-type vacuole / triose-phosphate isomerase / triose-phosphate isomerase activity / chloroplast stroma / response to zinc ion / chloroplast / gluconeogenesis ...plant-type cell wall / plasmodesma / apoplast / plant-type vacuole / triose-phosphate isomerase / triose-phosphate isomerase activity / chloroplast stroma / response to zinc ion / chloroplast / gluconeogenesis / glycolytic process / copper ion binding / mitochondrion / plasma membrane / cytosol Similarity search - Function | ||||||
Biological species | Arabidopsis thaliana (thale cress) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.64 Å | ||||||
Authors | Jimenez-Sandoval, P. / Fuentes-Pascacio, A. / Diaz-Quezada, C. / Torres-Larios, A. / Brieba, L.G. | ||||||
Citation | Journal: Plant J. / Year: 2019 Title: Structural basis for the modulation of plant cytosolic triosephosphate isomerase activity by mimicry of redox-based modifications. Authors: Castro-Torres, E. / Jimenez-Sandoval, P. / Romero-Romero, S. / Fuentes-Pascacio, A. / Lopez-Castillo, L.M. / Diaz-Quezada, C. / Fernandez-Velasco, D.A. / Torres-Larios, A. / Brieba, L.G. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6nxx.cif.gz | 143.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6nxx.ent.gz | 88.5 KB | Display | PDB format |
PDBx/mmJSON format | 6nxx.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/nx/6nxx ftp://data.pdbj.org/pub/pdb/validation_reports/nx/6nxx | HTTPS FTP |
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-Related structure data
Related structure data | 6nxqC 6nxrC 6nxsC 6nxwC 6nxyC 4obtS 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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-Components
#1: Protein | Mass: 27515.355 Da / Num. of mol.: 2 / Mutation: C218K Source method: isolated from a genetically manipulated source Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: CTIMC, At3g55440, T22E16.100 / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: P48491, triose-phosphate isomerase #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: 2.83 Å3/Da / Density % sol: 56.49 % |
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Crystal grow | Temperature: 292 K / Method: vapor diffusion, hanging drop Details: 0.03 M Diethylene glycol; 0.03 M Triethylene glycol; 0.03 M Tetraethylene glycol; 0.03 M Pentaethyleneglycol, 0.1 M HEPES/MOPS pH 7.5, 12.5 % v/v MPD; 12.5 % PEG 1000; 12.5 % w/v PEG 3350 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.9787 Å |
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jun 26, 2017 |
Radiation | Monochromator: C(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9787 Å / Relative weight: 1 |
Reflection | Resolution: 1.64→67.41 Å / Num. obs: 75395 / % possible obs: 99.7 % / Redundancy: 9.5 % / Biso Wilson estimate: 17.31 Å2 / Net I/σ(I): 17.2 |
Reflection shell | Resolution: 1.64→1.66 Å |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4OBT Resolution: 1.64→67.02 Å / SU ML: 0.1477 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 19.9051
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 21.91 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.64→67.02 Å
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Refine LS restraints |
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LS refinement shell |
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