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- PDB-6up1: Triosephosphate isomerase deficiency: Effect of F240L mutation on... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6up1 | ||||||
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Title | Triosephosphate isomerase deficiency: Effect of F240L mutation on enzyme structure | ||||||
![]() | Triosephosphate isomerase![]() | ||||||
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Function / homology | ![]() methylglyoxal biosynthetic process / ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Romero, J.M. | ||||||
![]() | ![]() Title: Triosephosphate isomerase deficiency: Effect of F240L mutation on enzyme structure. Authors: Romero, J.M. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 115.3 KB | Display | ![]() |
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PDB format | ![]() | 87 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | ![]() Mass: 26983.744 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() References: UniProt: P60174, ![]() ![]() #2: Chemical | ![]() #3: Water | ChemComp-HOH / | ![]() Has ligand of interest | N | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.17 Å3/Da / Density % sol: 43.22 % |
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Crystal grow![]() | Temperature: 283.15 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 0.1 M HEPES pH 7.5, 20% PEG 4000, and 10% 2-propanol PH range: 7.0-8.0 / Temp details: l |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | ||||||||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | ||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Nov 15, 2018 | ||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength![]() | ||||||||||||||||||||||||||||||
Reflection | Resolution: 1.83→58.63 Å / Num. obs: 41032 / % possible obs: 99.1 % / Redundancy: 5 % / CC1/2: 0.992 / Rmerge(I) obs: 0.101 / Rpim(I) all: 0.048 / Rrim(I) all: 0.113 / Net I/σ(I): 9.7 | ||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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Processing
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Refinement | Method to determine structure![]() ![]() Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 97.03 Å2 / Biso mean: 25.069 Å2 / Biso min: 9.83 Å2
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Refinement step | Cycle: final / Resolution: 1.83→58.63 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.83→1.877 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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