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Yorodumi- PDB-4kxy: Human transketolase in complex with ThDP analogue (R)-2-(1,2-dihy... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4kxy | ||||||
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Title | Human transketolase in complex with ThDP analogue (R)-2-(1,2-dihydroxyethyl)-3-deaza-ThDP | ||||||
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 / glyceraldehyde-3-phosphate biosynthetic process / pentose-phosphate shunt / 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 / glyceraldehyde-3-phosphate biosynthetic process / pentose-phosphate shunt / 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: 1.26 Å | ||||||
Authors | Neumann, P. / Luedtke, S. / Erixon, K.M. / Leeper, F. / Kluger, R. / 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 | 4kxy.cif.gz | 579 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4kxy.ent.gz | 468.8 KB | Display | PDB format |
PDBx/mmJSON format | 4kxy.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/kx/4kxy ftp://data.pdbj.org/pub/pdb/validation_reports/kx/4kxy | HTTPS FTP |
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-Related structure data
Related structure data | 4kxuC 4kxvC 4kxwC 4kxxC 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
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 69647.461 Da / Num. of mol.: 2 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, 1497 molecules
#2: Chemical | ChemComp-EDO / #3: Chemical | #4: Chemical | #5: Chemical | #6: Chemical | #7: 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: 2.09 Å3/Da / Density % sol: 41.14 % |
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Crystal grow | Temperature: 293 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 293K |
-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: 1.26→30 Å / Num. all: 307778 / Num. obs: 307778 / % possible obs: 99.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 3.1 % / Biso Wilson estimate: 14.88 Å2 / Rmerge(I) obs: 0.066 / Net I/σ(I): 13.07 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS Starting model: PDB ENTRY 3MOS Resolution: 1.26→30 Å / Num. parameters: 105540 / Num. restraintsaints: 114390 / Occupancy max: 1.64 / Occupancy min: 0.03 / 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: 159.88 Å2 / Biso mean: 16.4439 Å2 / Biso min: -0.08 Å2 | |||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.26→30 Å
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Refine LS restraints |
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