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- PDB-4kxv: Human transketolase in covalent complex with donor ketose D-xylul... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4kxv | |||||||||
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Title | Human transketolase in covalent complex with donor ketose D-xylulose-5-phosphate, crystal 1 | |||||||||
![]() | Transketolase | |||||||||
![]() | TRANSFERASE / thiamin diphosphate / enzyme catalysis / pentose phosphate pathway | |||||||||
Function / homology | ![]() xylulose 5-phosphate biosynthetic process / Insulin effects increased synthesis of Xylulose-5-Phosphate / Pentose phosphate pathway / transketolase / transketolase activity / pentose-phosphate shunt, non-oxidative branch / pentose-phosphate shunt / NFE2L2 regulates pentose phosphate pathway genes / glyceraldehyde-3-phosphate biosynthetic process / regulation of growth ...xylulose 5-phosphate biosynthetic process / Insulin effects increased synthesis of Xylulose-5-Phosphate / Pentose phosphate pathway / transketolase / transketolase activity / pentose-phosphate shunt, non-oxidative branch / pentose-phosphate shunt / NFE2L2 regulates pentose phosphate pathway genes / glyceraldehyde-3-phosphate biosynthetic process / regulation of growth / thiamine pyrophosphate binding / peroxisome / vesicle / nuclear body / calcium ion binding / endoplasmic reticulum membrane / magnesium ion binding / protein homodimerization activity / extracellular exosome / nucleoplasm / cytosol Similarity search - Function | |||||||||
Biological species | ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Neumann, P. / Luedtke, S. / Ficner, R. / Tittmann, K. | |||||||||
![]() | ![]() Title: Sub-angstrom-resolution crystallography reveals physical distortions that enhance reactivity of a covalent enzymatic intermediate. Authors: Ludtke, S. / Neumann, P. / Erixon, K.M. / Leeper, F. / Kluger, R. / Ficner, R. / Tittmann, K. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 317.1 KB | Display | ![]() |
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PDB format | ![]() | 251.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 766.4 KB | Display | ![]() |
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Full document | ![]() | 782.4 KB | Display | |
Data in XML | ![]() | 36.7 KB | Display | |
Data in CIF | ![]() | 59 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4kxuC ![]() 4kxwC ![]() 4kxxC ![]() 4kxyC ![]() 3mosS 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
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 69647.461 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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-Non-polymers , 5 types, 969 molecules ![](data/chem/img/CA.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/TPP.gif)
![](data/chem/img/DX5.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/TPP.gif)
![](data/chem/img/DX5.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-CA / | ||||||
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#3: Chemical | ChemComp-EDO / #4: Chemical | ChemComp-TPP / | #5: Chemical | ChemComp-DX5 / | #6: Water | ChemComp-HOH / | |
-Details
Nonpolymer details | DX5 A1011 IS A HYDROLYZED |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.13 Å3/Da / Density % sol: 42.3 % |
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Crystal grow | Temperature: 279 K / Method: vapor diffusion, hanging drop / pH: 7.9 Details: Reservoir mixture of 13.5-15 % PEG 6000 (w/v), 4% PEG 400 (v/v), 2 % glycerol (v/v) , pH 7.9, VAPOR DIFFUSION, HANGING DROP, temperature 279.0K |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 22, 2011 / Details: mirrors | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.93939 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 0.97→30 Å / Num. all: 308592 / Num. obs: 301825 / % possible obs: 91.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 3.9 % / Biso Wilson estimate: 9.245 Å2 / Rmerge(I) obs: 0.052 / Net I/σ(I): 14.98 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 3MOS Resolution: 0.97→30 Å / Num. parameters: 56477 / Num. restraintsaints: 60863 / Occupancy max: 1.05 / Occupancy min: 0.06 / Cross valid method: FREE R / σ(F): 0 / σ(I): 0 / Stereochemistry target values: ENGH AND HUBER Details: ANISOTROPIC REFINEMENT REDUCED FREE R (NO CUTOFF) BY ?
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Solvent computation | Solvent model: MOEWS & KRETSINGER, J.MOL.BIOL.91(1973)201-228 | |||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 185.75 Å2 / Biso mean: 13.8392 Å2 / Biso min: 1.45 Å2 | |||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 0.97→30 Å
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Refine LS restraints |
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