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- PDB-5x4w: Mutant human thymidylate synthase A191K crystallized in a sulfate... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5x4w | ||||||
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Title | Mutant human thymidylate synthase A191K crystallized in a sulfate-free condition | ||||||
![]() | Thymidylate synthase | ||||||
![]() | TRANSFERASE / methyltransferase | ||||||
Function / homology | ![]() uracil metabolic process / response to organophosphorus / intestinal epithelial cell maturation / response to folic acid / Interconversion of nucleotide di- and triphosphates / thymidylate synthase / response to vitamin A / sequence-specific mRNA binding / cartilage development / tetrahydrofolate interconversion ...uracil metabolic process / response to organophosphorus / intestinal epithelial cell maturation / response to folic acid / Interconversion of nucleotide di- and triphosphates / thymidylate synthase / response to vitamin A / sequence-specific mRNA binding / cartilage development / tetrahydrofolate interconversion / thymidylate synthase activity / folic acid binding / dTMP biosynthetic process / dTTP biosynthetic process / DNA biosynthetic process / G1/S-Specific Transcription / developmental growth / dihydrofolate reductase activity / response to glucocorticoid / mRNA regulatory element binding translation repressor activity / response to cytokine / response to progesterone / liver regeneration / response to toxic substance / circadian rhythm / methylation / response to ethanol / mitochondrial inner membrane / negative regulation of translation / mitochondrial matrix / response to xenobiotic stimulus / protein homodimerization activity / mitochondrion / nucleus / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Chen, D. / Jansson, A. / Larsson, A. / Nordlund, P. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Structural analyses of human thymidylate synthase reveal a site that may control conformational switching between active and inactive states Authors: Chen, D. / Jansson, A. / Sim, D. / Larsson, A. / Nordlund, P. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 74 KB | Display | ![]() |
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PDB format | ![]() | 53.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 437.3 KB | Display | ![]() |
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Full document | ![]() | 438.2 KB | Display | |
Data in XML | ![]() | 13.4 KB | Display | |
Data in CIF | ![]() | 18.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5x4xC ![]() 5x4yC ![]() 5x5aC ![]() 5x5dC ![]() 5x5qC ![]() 5x66C ![]() 5x67C ![]() 5x69C ![]() 1hw3S C: citing same article ( S: Starting model for refinement |
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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
#1: Protein | Mass: 35908.113 Da / Num. of mol.: 1 / Mutation: A191K Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() | ||
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#2: Chemical | #3: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.19 Å3/Da / Density % sol: 61.46 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / Details: 100mM HEPES, pH 7.0, 10% PEG 6000 |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 7, 2014 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9537 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.1→82.783 Å / Num. all: 24955 / Num. obs: 24955 / % possible obs: 99.9 % / Redundancy: 10.2 % / Rpim(I) all: 0.034 / Rrim(I) all: 0.108 / Rsym value: 0.102 / Net I/av σ(I): 4.7 / Net I/σ(I): 15 / Num. measured all: 254681 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1HW3 Resolution: 2.1→82.78 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.954 / SU B: 3.292 / SU ML: 0.086 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.138 / ESU R Free: 0.127 / Stereochemistry target values: MAXIMUM LIKELIHOOD 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 / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 123.02 Å2 / Biso mean: 32.789 Å2 / Biso min: 14.18 Å2
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Refinement step | Cycle: final / Resolution: 2.1→82.78 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.1→2.155 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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