[English] 日本語
Yorodumi- PDB-4kxw: Human transketolase in covalent complex with donor ketose D-xylul... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4kxw | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | Human transketolase in covalent complex with donor ketose D-xylulose-5-phosphate, crystal 2 | |||||||||
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: 0.97 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 |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 4kxw.cif.gz | 327.1 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb4kxw.ent.gz | 261.1 KB | Display | PDB format |
PDBx/mmJSON format | 4kxw.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/kx/4kxw ftp://data.pdbj.org/pub/pdb/validation_reports/kx/4kxw | HTTPS FTP |
---|
-Related structure data
Related structure data | 4kxuC 4kxvC 4kxxC 4kxyC 3mosS S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| |||||||||
---|---|---|---|---|---|---|---|---|---|---|
1 |
| |||||||||
Unit cell |
| |||||||||
Components on special symmetry positions |
|
-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 |
---|
-Non-polymers , 6 types, 980 molecules
#2: Chemical | ChemComp-MG / | ||||||||
---|---|---|---|---|---|---|---|---|---|
#3: Chemical | ChemComp-EDO / #4: Chemical | ChemComp-NA / | #5: Chemical | ChemComp-TPP / | #6: Chemical | #7: Water | ChemComp-HOH / | |
-Details
Nonpolymer details | DX5 A1016 IS A HYDROLYZED |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.13 Å3/Da / Density % sol: 42.3 % |
---|---|
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 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.93939 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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: 312019 / Num. obs: 305775 / % possible obs: 92.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 3.3 % / Biso Wilson estimate: 10.555 Å2 / Rmerge(I) obs: 0.047 / Net I/σ(I): 14.23 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
|
-Processing
Software |
| |||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: FOURIER SYNTHESIS Starting model: PDB ENTRY 3MOS Resolution: 0.97→30 Å / Num. parameters: 58206 / Num. restraintsaints: 62846 / Occupancy max: 1 / Occupancy min: 0.03 / Cross valid method: FREE R / σ(F): 0 / σ(I): 0 / Stereochemistry target values: ENGH AND HUBER
| |||||||||||||||||||||||||||||||||
Solvent computation | Solvent model: MOEWS & KRETSINGER, J.MOL.BIOL.91(1973)201-228 | |||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 229.73 Å2 / Biso mean: 15.9484 Å2 / Biso min: 2.85 Å2 | |||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 0.97→30 Å
| |||||||||||||||||||||||||||||||||
Refine LS restraints |
|