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Yorodumi- PDB-6qxh: Crystal structure of His-tag human thymidylate synthase (HT-hTS) ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6qxh | ||||||
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Title | Crystal structure of His-tag human thymidylate synthase (HT-hTS) in complex with dUMP | ||||||
Components | Thymidylate synthase | ||||||
Keywords | TRANSFERASE / human thymidylate synthase / folate pathway / substrate / dUMP | ||||||
Function / homology | Function and homology information 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 / response to glucocorticoid / mRNA regulatory element binding translation repressor activity / response to cytokine / response to progesterone / liver regeneration / response to toxic substance / circadian rhythm / response to ethanol / methylation / mitochondrial inner membrane / negative regulation of translation / mitochondrial matrix / response to xenobiotic stimulus / protein homodimerization activity / mitochondrion / nucleus / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.04 Å | ||||||
Authors | Pozzi, C. / Mangani, M. | ||||||
Funding support | 1items
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Citation | Journal: Molecules / Year: 2019 Title: Structural Comparison ofEnterococcus faecalisand Human Thymidylate Synthase Complexes with the Substrate dUMP and Its Analogue FdUMP Provides Hints about Enzyme Conformational Variabilities. Authors: Pozzi, C. / Ferrari, S. / Luciani, R. / Tassone, G. / Costi, M.P. / Mangani, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6qxh.cif.gz | 364 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6qxh.ent.gz | 300.1 KB | Display | PDB format |
PDBx/mmJSON format | 6qxh.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6qxh_validation.pdf.gz | 1.3 MB | Display | wwPDB validaton report |
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Full document | 6qxh_full_validation.pdf.gz | 1.3 MB | Display | |
Data in XML | 6qxh_validation.xml.gz | 33.8 KB | Display | |
Data in CIF | 6qxh_validation.cif.gz | 47.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qx/6qxh ftp://data.pdbj.org/pub/pdb/validation_reports/qx/6qxh | HTTPS FTP |
-Related structure data
Related structure data | 6qxgC 6qxsC 6qyaC 1hwyS C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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Unit cell |
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-Components
-Protein , 1 types, 3 molecules ABC
#1: Protein | Mass: 37214.547 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: TYMS, TS, OK/SW-cl.29 / Plasmid: pQE80L / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P04818, thymidylate synthase |
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-Non-polymers , 5 types, 211 molecules
#2: Chemical | #3: Chemical | ChemComp-PEG / | #4: Chemical | ChemComp-CL / | #5: Chemical | ChemComp-SO4 / | #6: 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: 2.59 Å3/Da / Density % sol: 52.43 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 9 Details: 27-30 % wt/vol PEG4000, 30 mM ammonium sulfate and 0.1 M TRIS, pH 9 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P14 (MX2) / Wavelength: 0.97625 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 1, 2015 |
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97625 Å / Relative weight: 1 |
Reflection | Resolution: 2.04→34.19 Å / Num. obs: 62630 / % possible obs: 97 % / Observed criterion σ(I): 2 / Redundancy: 6.3 % / Biso Wilson estimate: 43.18 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.066 / Rpim(I) all: 0.028 / Rrim(I) all: 0.072 / Net I/σ(I): 12.8 |
Reflection shell | Resolution: 2.04→2.15 Å / Redundancy: 6.4 % / Rmerge(I) obs: 0.484 / Mean I/σ(I) obs: 3.3 / Num. unique obs: 9114 / CC1/2: 0.937 / Rpim(I) all: 0.206 / Rrim(I) all: 0.528 / % possible all: 97.2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1HWY Resolution: 2.04→34.19 Å / Cor.coef. Fo:Fc: 0.973 / Cor.coef. Fo:Fc free: 0.956 / SU B: 16.95 / SU ML: 0.202 / Cross valid method: THROUGHOUT / ESU R: 0.192 / ESU R Free: 0.175
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 69.393 Å2
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Refine analyze | Luzzati coordinate error obs: 0.356 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.04→34.19 Å
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Refine LS restraints |
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