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- PDB-6nxq: Crystal structure of Arabidopsis thaliana cytosolic triosephospha... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6nxq | ||||||
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Title | Crystal structure of Arabidopsis thaliana cytosolic triosephosphate isomerase C13A mutant | ||||||
![]() | Triosephosphate isomerase, cytosolic![]() | ||||||
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Function / homology | ![]() plant-type cell wall / ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() Similarity search - Function | ||||||
Biological species | ![]() ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Jimenez-Sandoval, P. / Diaz-Quezada, C. / Torres-Larios, A. / Brieba, L.G. | ||||||
![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 111.8 KB | Display | ![]() |
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PDB format | ![]() | 84.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 6nxrC ![]() 6nxsC ![]() 6nxwC ![]() 6nxxC ![]() 6nxyC ![]() 4obtS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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Unit cell |
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Components on special symmetry positions |
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Components
#1: Protein | ![]() Mass: 27457.254 Da / Num. of mol.: 1 / Mutation: C13A Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() ![]() ![]() |
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#2: Chemical | ChemComp-NA / |
#3: Water | ChemComp-HOH / ![]() |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.77 Å3/Da / Density % sol: 55.6 % |
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Crystal grow![]() | Temperature: 292 K / Method: vapor diffusion, hanging drop Details: 0.2 M Magnesium chloride hexahydrate, 0.1 M TRIS hydrochloride 8.5, 30 % w/v Polyethylene glycol 4,000 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() |
Detector | Type: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Aug 13, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 1.96→62.47 Å / Num. obs: 22354 / % possible obs: 99.4 % / Redundancy: 5.9 % / CC1/2: 0.998 / Rmerge(I) obs: 0.088 / Rpim(I) all: 0.039 / Rrim(I) all: 0.096 / Net I/σ(I): 15.1 |
Reflection shell | Resolution: 1.96→2.01 Å / Redundancy: 5.4 % / Rmerge(I) obs: 0.434 / Num. unique obs: 1502 / CC1/2: 0.898 / Rpim(I) all: 0.2 / Rrim(I) all: 0.48 / % possible all: 97.1 |
-Phasing
Phasing![]() | Method: ![]() | |||||||||
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Phasing MR |
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Processing
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Refinement | Method to determine structure![]() ![]() Starting model: 4OBT Resolution: 1.96→62.47 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.944 / SU B: 5.774 / SU ML: 0.086 / SU R Cruickshank DPI: 0.1347 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.135 / ESU R Free: 0.124 Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
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Solvent computation | Ion probe radii: 0.9 Å / Shrinkage radii: 0.9 Å / VDW probe radii: 1.5 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 67.23 Å2 / Biso mean: 19.118 Å2 / Biso min: 11.91 Å2
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Refinement step | Cycle: final / Resolution: 1.96→62.47 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.96→2.011 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Origin x: -14.014 Å / Origin y: -19.547 Å / Origin z: 7.988 Å
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