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Yorodumi- PDB-1tsn: THYMIDYLATE SYNTHASE TERNARY COMPLEX WITH FDUMP AND METHYLENETETR... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1tsn | |||||||||
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Title | THYMIDYLATE SYNTHASE TERNARY COMPLEX WITH FDUMP AND METHYLENETETRAHYDROFOLATE | |||||||||
Components | THYMIDYLATE SYNTHASE | |||||||||
Keywords | METHYLTRANSFERASE / TRANSFERASE | |||||||||
Function / homology | Function and homology information thymidylate synthase / thymidylate synthase activity / dTMP biosynthetic process / dTTP biosynthetic process / response to radiation / regulation of translation / methylation / magnesium ion binding / protein homodimerization activity / RNA binding ...thymidylate synthase / thymidylate synthase activity / dTMP biosynthetic process / dTTP biosynthetic process / response to radiation / regulation of translation / methylation / magnesium ion binding / protein homodimerization activity / RNA binding / cytosol / cytoplasm Similarity search - Function | |||||||||
Biological species | Escherichia coli (E. coli) | |||||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.2 Å | |||||||||
Authors | Hyatt, D.C. / Maley, F. / Montfort, W.R. | |||||||||
Citation | Journal: Biochemistry / Year: 1997 Title: Use of strain in a stereospecific catalytic mechanism: crystal structures of Escherichia coli thymidylate synthase bound to FdUMP and methylenetetrahydrofolate. Authors: Hyatt, D.C. / Maley, F. / Montfort, W.R. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1tsn.cif.gz | 71.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1tsn.ent.gz | 52.7 KB | Display | PDB format |
PDBx/mmJSON format | 1tsn.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ts/1tsn ftp://data.pdbj.org/pub/pdb/validation_reports/ts/1tsn | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 30559.666 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: TERNARY COMPLEX WITH FDUMP (INHIBITOR) AND METHYLENETETRAHYDROFOLATE (COFACTOR) Source: (gene. exp.) Escherichia coli (E. coli) References: UniProt: P00470, UniProt: P0A884*PLUS, thymidylate synthase |
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#2: Chemical | ChemComp-PO4 / |
#3: Chemical | ChemComp-UFP / |
#4: Chemical | ChemComp-C2F / |
#5: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.83 Å3/Da / Density % sol: 56.52 % | ||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Method: vapor diffusion / pH: 8 Details: CRYSTALLIZED BY VAPOR DIFFUSION FROM A SOLUTION OF 8MG/ML PROTEIN, 2MM FDUMP, 10MM CH2THF, 20MM PHOSPHATE PH 8.0, 4MM DTT, AND 1.05M AMMONIUM SULFATE; EQUILIBRATED AGAINST A SOLUTION OF 2. ...Details: CRYSTALLIZED BY VAPOR DIFFUSION FROM A SOLUTION OF 8MG/ML PROTEIN, 2MM FDUMP, 10MM CH2THF, 20MM PHOSPHATE PH 8.0, 4MM DTT, AND 1.05M AMMONIUM SULFATE; EQUILIBRATED AGAINST A SOLUTION OF 2.10M AMMONIUM SULFATE, 20MM PHOSPHATE PH 8.0, AND 4MM DTT., vapor diffusion | ||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 298 K |
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Diffraction source | Source: ROTATING ANODE / Type: ENRAF-NONIUS FR571 / Wavelength: 1.5418 |
Detector | Type: ENRAF-NONIUS FAST / Detector: DIFFRACTOMETER / Date: May 1, 1996 |
Radiation | Monochromator: GRAPHITE(002) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→9 Å / Num. obs: 18104 / % possible obs: 98.4 % / Observed criterion σ(I): 0 / Redundancy: 4.1 % / Rsym value: 0.095 / Net I/σ(I): 6.4 |
Reflection shell | Resolution: 2.2→2.29 Å / Redundancy: 3.4 % / Mean I/σ(I) obs: 1.9 / Rsym value: 0.355 / % possible all: 98.5 |
Reflection | *PLUS Num. measured all: 76346 / Rmerge(I) obs: 0.095 |
Reflection shell | *PLUS Rmerge(I) obs: 0.36 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: TS.FDUMP.CB3717 Resolution: 2.2→9 Å / σ(F): 0
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Displacement parameters | Biso mean: 21 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.2→9 Å
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Refine LS restraints |
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Software | *PLUS Name: GPRLSA / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Rfactor all: 0.178 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS |