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Yorodumi- PDB-6ojv: Crystal structure of human thymidylate synthase delta(7-29) in co... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6ojv | |||||||||
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Title | Crystal structure of human thymidylate synthase delta(7-29) in complex with dUMP and 2-amino-4-oxo-4,7-dihydro-pyrrolo[2,3-d]pyrimidine-methyl-phenyl-L-glutamic acid | |||||||||
Components | Thymidylate synthase,Thymidylate synthase | |||||||||
Keywords | TRANSFERASE/TRANSFERASE INHIBITOR / Inhibitor / TS / TS-DHFR / TRANSFERASE / TRANSFERASE-TRANSFERASE INHIBITOR complex | |||||||||
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 / liver regeneration / mRNA regulatory element binding translation repressor activity / response to cytokine / response to progesterone / circadian rhythm / response to toxic substance / methylation / response to ethanol / negative regulation of translation / mitochondrial inner membrane / mitochondrial matrix / response to xenobiotic stimulus / protein homodimerization activity / mitochondrion / nucleus / cytoplasm / cytosol Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.593 Å | |||||||||
Authors | Czyzyk, D.J. / Anderson, K.S. / Valhondo, M. / Jorgensen, W.L. | |||||||||
Funding support | United States, 2items
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Citation | Journal: Febs Lett. / Year: 2019 Title: Understanding the structural basis of species selective, stereospecific inhibition for Cryptosporidium and human thymidylate synthase. Authors: Czyzyk, D.J. / Valhondo, M. / Jorgensen, W.L. / Anderson, K.S. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6ojv.cif.gz | 235.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6ojv.ent.gz | 188.3 KB | Display | PDB format |
PDBx/mmJSON format | 6ojv.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6ojv_validation.pdf.gz | 2.5 MB | Display | wwPDB validaton report |
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Full document | 6ojv_full_validation.pdf.gz | 2.6 MB | Display | |
Data in XML | 6ojv_validation.xml.gz | 42.6 KB | Display | |
Data in CIF | 6ojv_validation.cif.gz | 54.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/oj/6ojv ftp://data.pdbj.org/pub/pdb/validation_reports/oj/6ojv | HTTPS FTP |
-Related structure data
Related structure data | 6ojsC 6ojuC 1hzwS 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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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 33189.070 Da / Num. of mol.: 4 / Fragment: residues 30-313 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: TYMS, TS, OK/SW-cl.29 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / Variant (production host): TX-61 / References: UniProt: P04818, thymidylate synthase #2: Chemical | ChemComp-UMP / #3: Chemical | ChemComp-2XB / #4: 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: 2.6 Å3/Da / Density % sol: 52.7 % |
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Crystal grow | Temperature: 295.15 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: Well solution 5% PEG 8000, 40% MPD, and 0.1M Na cacodylate Drop ratio 1:1 Enzyme mix/well solution |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.97915 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jul 6, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97915 Å / Relative weight: 1 |
Reflection | Resolution: 2.59→50 Å / Num. obs: 41155 / % possible obs: 98.7 % / Redundancy: 6.6 % / CC1/2: 0.996 / Rsym value: 0.141 / Net I/σ(I): 12.75 |
Reflection shell | Resolution: 2.59→2.75 Å / Redundancy: 6.4 % / Mean I/σ(I) obs: 1.44 / Num. unique obs: 6486 / CC1/2: 0.807 / Rsym value: 1.16 / % possible all: 97.1 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1HZW Resolution: 2.593→48.556 Å / SU ML: 0.47 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 35.32 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.593→48.556 Å
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Refine LS restraints |
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LS refinement shell |
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