+Open data
-Basic information
Entry | Database: PDB / ID: 2tdm | |||||||||
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Title | STRUCTURE OF THYMIDYLATE SYNTHASE | |||||||||
Components | THYMIDYLATE SYNTHASE | |||||||||
Keywords | METHYLTRANSFERASE / TRANSFERASE | |||||||||
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: 2.55 Å | |||||||||
Authors | Finer-Moore, J. / Stroud, R.M. | |||||||||
Citation | Journal: J.Mol.Biol. / Year: 1993 Title: Refined structures of substrate-bound and phosphate-bound thymidylate synthase from Lactobacillus casei. Authors: Finer-Moore, J. / Fauman, E.B. / Foster, P.G. / Perry, K.M. / Santi, D.V. / Stroud, R.M. #1: 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. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2tdm.cif.gz | 77.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2tdm.ent.gz | 59 KB | Display | PDB format |
PDBx/mmJSON format | 2tdm.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/td/2tdm ftp://data.pdbj.org/pub/pdb/validation_reports/td/2tdm | 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
#1: Protein | Mass: 36630.453 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Lactobacillus casei (bacteria) Description: STRAIN CHI-2913 LACKS A THYMIDYLATE SYNTHASE GENE 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 / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.92 Å3/Da / Density % sol: 55 % | ||||||||||||||||||||
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Crystal grow | pH: 7.4 / Details: pH 7.4 | ||||||||||||||||||||
Crystal grow | *PLUS Method: vapor diffusion | ||||||||||||||||||||
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 RUH2R / Wavelength: 1.5418 |
Detector | Type: SIEMENS / Detector: AREA DETECTOR / Date: Nov 1, 1990 |
Radiation | Monochromator: GRAPHITE(002) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.55→50 Å / Num. obs: 12591 / % possible obs: 83 % / Observed criterion σ(I): 0 / Redundancy: 3.7 % / Rsym value: 0.156 / Net I/σ(I): 9.4 |
Reflection shell | Resolution: 2.55→2.7 Å / Redundancy: 2 % / Mean I/σ(I) obs: 0.8 / Rsym value: 0.52 / % possible all: 65 |
Reflection | *PLUS Num. measured all: 46338 / Rmerge(I) obs: 0.156 |
Reflection shell | *PLUS % possible obs: 65 % / Rmerge(I) obs: 0.52 |
-Processing
Software |
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Refinement | Resolution: 2.55→7 Å / σ(F): 2 Details: THE SIDE CHAIN OF ARG 23 IS IN TWO HALF-OCCUPIED CONFORMATIONS IN THE CRYSTAL STRUCTURE.
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Displacement parameters | Biso mean: 31 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.55→7 Å
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Refine LS restraints |
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Xplor file |
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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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