+Open data
-Basic information
Entry | Database: PDB / ID: 1tsy | ||||||
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Title | THYMIDYLATE SYNTHASE R179K MUTANT | ||||||
Components | THYMIDYLATE SYNTHASE | ||||||
Keywords | TRANSFERASE / METHYLTRANSFERASE / NUCLEOTIDE BIOSYNTHESIS | ||||||
Function / homology | Function and homology information thymidylate synthase / thymidylate synthase activity / dTMP biosynthetic process / dTTP biosynthetic process / methylation / cytosol Similarity search - Function | ||||||
Biological species | Lactobacillus casei (bacteria) | ||||||
Method | X-RAY DIFFRACTION / Resolution: 2.2 Å | ||||||
Authors | Finer-Moore, J. / Stroud, R.M. | ||||||
Citation | Journal: Protein Eng. / Year: 1996 Title: Contribution of a salt bridge to binding affinity and dUMP orientation to catalytic rate: mutation of a substrate-binding arginine in thymidylate synthase. Authors: Finer-Moore, J.S. / Fauman, E.B. / Morse, R.J. / Santi, D.V. / Stroud, R.M. #1: Journal: Faseb J. / Year: 1993 Title: Stereochemistry of a Multistep(Slash)Bipartite Methyl Transfer Reaction: Thymidylate Synthase Authors: Stroud, R.M. / Finer-Moore, J.S. #2: Journal: J.Mol.Biol. / Year: 1993 Title: Refined Structures of Substrate-Bound and Phosphate-Bound Thymidylate Synthase from Lactobacillus Casei Authors: Finer-Moore, J.S. / Fauman, E.B. / Foster, P.G. / Perry, K.M. / Santi, D.V. / Stroud, R.M. #3: Journal: Science / Year: 1987 Title: Atomic Structure of Thymidylate Synthase: Target for Rational Drug Design Authors: Hardy, L.W. / Finer-Moore, J.S. / Montfort, W.R. / Jones, M.O. / Santi, D.V. / Stroud, R.M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1tsy.cif.gz | 78.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1tsy.ent.gz | 59.1 KB | Display | PDB format |
PDBx/mmJSON format | 1tsy.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ts/1tsy ftp://data.pdbj.org/pub/pdb/validation_reports/ts/1tsy | 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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Details | SYMMETRY THE CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS PRESENTED BELOW GENERATE THE SUBUNITS OF THE POLYMERIC MOLECULE. THE DIMER IS GENERATED BY A CRYSTALLOGRAPHIC TWO-FOLD, THE TRANSFORMATION MATRIX MUST BE APPLY TO FRACTIONAL COORDINATES. SYMMETRY1 1 -1.000000 1.000000 0.000000 0.00000 SYMMETRY2 1 0.000000 1.000000 0.000000 0.00000 SYMMETRY3 1 0.000000 0.000000 -1.000000 -0.50000 |
-Components
#1: Protein | Mass: 36602.441 Da / Num. of mol.: 1 / Mutation: R179K Source method: isolated from a genetically manipulated source Source: (gene. exp.) Lactobacillus casei (bacteria) / Description: PURCHASED FROM SIGMA / Plasmid: PKPTSD / Production host: Escherichia coli (E. coli) / Strain (production host): CHI-2913 / References: UniProt: P00469, thymidylate synthase |
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#2: Chemical | ChemComp-UMP / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.96 Å3/Da / Density % sol: 58.46 % | ||||||||||||||||||||||||||||||||||||||||
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Crystal grow | pH: 7.2 / Details: pH 7.2 | ||||||||||||||||||||||||||||||||||||||||
Crystal | *PLUS Density % sol: 55 % | ||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 295 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.5418 Å |
Detector | Type: RIGAKU / Detector: IMAGE PLATE / Date: Jun 13, 1995 / Details: COLLIMATOR |
Radiation | Monochromator: GRAPHITE CRYSTAL / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→50 Å / Num. obs: 21363 / % possible obs: 91 % / Observed criterion σ(I): 0 / Redundancy: 4 % / Rmerge(I) obs: 0.088 |
Reflection | *PLUS Num. measured all: 90968 / Rmerge(I) obs: 0.088 |
-Processing
Software |
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Refinement | Resolution: 2.2→7 Å / σ(F): 1
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Displacement parameters | Biso mean: 36.2 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.2→7 Å
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Refine LS restraints |
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Software | *PLUS Name: X-PLOR / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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