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Yorodumi- PDB-4kxx: Human transketolase in covalent complex with donor ketose D-sedoh... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4kxx | |||||||||
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Title | Human transketolase in covalent complex with donor ketose D-sedoheptulose-7-phosphate | |||||||||
Components | Transketolase | |||||||||
Keywords | TRANSFERASE / thiamin diphosphate / enzyme catalysis / pentose phosphate pathway | |||||||||
Function / homology | Function and homology information 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 / glyceraldehyde-3-phosphate biosynthetic process / NFE2L2 regulates pentose phosphate pathway genes / 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 / glyceraldehyde-3-phosphate biosynthetic process / NFE2L2 regulates pentose phosphate pathway genes / 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 | Homo sapiens (human) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.03 Å | |||||||||
Authors | Neumann, P. / Luedtke, S. / Ficner, R. / Tittmann, K. | |||||||||
Citation | Journal: Nat Chem / Year: 2013 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4kxx.cif.gz | 314.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4kxx.ent.gz | 248.9 KB | Display | PDB format |
PDBx/mmJSON format | 4kxx.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/kx/4kxx ftp://data.pdbj.org/pub/pdb/validation_reports/kx/4kxx | HTTPS FTP |
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-Related structure data
Related structure data | 4kxuC 4kxvC 4kxwC 4kxyC 3mosS 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 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.) Homo sapiens (human) / Gene: TKT / Plasmid: pET-28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P29401, transketolase |
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-Non-polymers , 6 types, 801 molecules
#2: Chemical | ChemComp-1Y7 / ( | ||||||
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#3: Chemical | ChemComp-TPP / | ||||||
#4: Chemical | ChemComp-EDO / #5: Chemical | ChemComp-MG / | #6: Chemical | ChemComp-NA / | #7: Water | ChemComp-HOH / | |
-Details
Nonpolymer details | 1Y7 A1001 IS A HYDROLYZED |
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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: 2.13 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: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.9841 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: MARMOSAIC 225 mm CCD / 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: 0.9841 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.03→30 Å / Num. all: 279021 / Num. obs: 279021 / % possible obs: 98.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 3 % / Biso Wilson estimate: 9.994 Å2 / Rmerge(I) obs: 0.053 / Net I/σ(I): 15.48 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS Starting model: PDB ENTRY 3MOS Resolution: 1.03→30 Å / Num. parameters: 55907 / Num. restraintsaints: 60778 / Occupancy max: 1 / Occupancy min: 0.12 / Cross valid method: FREE R / σ(F): 0 / σ(I): 0 / Stereochemistry target values: ENGH AND HUBER
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Solvent computation | Solvent model: MOEWS & KRETSINGER, J.MOL.BIOL.91(1973)201-228 | |||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 186.83 Å2 / Biso mean: 15.5613 Å2 / Biso min: -0.08 Å2 | |||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.03→30 Å
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Refine LS restraints |
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