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Yorodumi- PDB-1nce: Crystal structure of a ternary complex of E. coli thymidylate syn... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1nce | ||||||
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Title | Crystal structure of a ternary complex of E. coli thymidylate synthase D169C with dUMP and the antifolate CB3717 | ||||||
Components | Thymidylate synthase | ||||||
Keywords | BIOSYNTHETIC PROTEIN / beta-sheet interface / protein-dUMP-cofactor analog complex / asymmetric dimer | ||||||
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 / cytosol Similarity search - Function | ||||||
Biological species | Escherichia coli (E. coli) Escherichia coli O157:H7 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / FOURIER SYNTHESIS / Resolution: 2.4 Å | ||||||
Authors | Birdsall, D.L. / Finer-Moore, J. / Stroud, R.M. | ||||||
Citation | Journal: Protein Eng. / Year: 2003 Title: The only active mutant of thymidylate synthase D169, a residue far from the site of methyl transfer, demonstrates the exquisite nature of enzyme specificity. Authors: Birdsall, D.L. / Finer-Moore, J. / Stroud, R.M. #1: Journal: Biochemistry / Year: 1998 Title: D221 in thymidylate synthase controls conformation change, and thereby opening of the imidazolidine Authors: Sage, C.R. / Michelitsch, M.D. / Stout, T.J. / Biermann, D. / Nissen, R. / Finer-Moore, J. / Stroud, R.M. #2: Journal: Biochemistry / Year: 1990 Title: Structure, multiple site binding, and segmental accommodation in thymidylate synthase on binding dUMP and an anti-folate Authors: Montfort, W.R. / Perry, K.M. / Fauman, E.B. / Finer-Moore, J.S. / Maley, G.F. / Hardy, L. / Maley, F. / 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 | 1nce.cif.gz | 125.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1nce.ent.gz | 97.4 KB | Display | PDB format |
PDBx/mmJSON format | 1nce.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/nc/1nce ftp://data.pdbj.org/pub/pdb/validation_reports/nc/1nce | HTTPS FTP |
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-Related structure data
Related structure data | 1kceS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Details | The biological assembly is a homodimer consisting of chains A and B |
-Components
#1: Protein | Mass: 30547.721 Da / Num. of mol.: 2 / Mutation: D169C Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli, Escherichia coli O157:H7 Genus: Escherichia, Escherichia / Species: , Escherichia coli / Strain: , O157:H7 / Gene: THYA OR B2827 OR Z4144 OR ECS3684 / Production host: Escherichia coli (E. coli) / References: UniProt: P0A884, thymidylate synthase #2: Chemical | #3: Chemical | #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: 52.65 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 9.1 Details: potassium phosphate, EDTA, ammonium sulfate, DTT, pH 9.1, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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: RIGAKU RU200 / Wavelength: 1.5418 |
Detector | Type: RIGAKU RAXIS II / Detector: IMAGE PLATE / Date: Dec 21, 1998 / Details: monochromater |
Radiation | Monochromator: graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.4→40 Å / Num. all: 24679 / Num. obs: 24679 / % possible obs: 100 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 8.7 % / Rmerge(I) obs: 0.174 / Net I/σ(I): 8.1 |
Reflection shell | Resolution: 2.4→2.55 Å / Mean I/σ(I) obs: 1.9 / % possible all: 100 |
Reflection | *PLUS % possible obs: 100 % |
-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS Starting model: PDB entry 1KCE with waters and ligands removed Resolution: 2.4→36.69 Å / Rfactor Rfree error: 0.006 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): -3 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 56.9659 Å2 / ksol: 0.334593 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 34.2 Å2
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Refine analyze | Luzzati coordinate error free: 0.37 Å / Luzzati sigma a free: 0.5 Å | ||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.4→36.69 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.4→2.55 Å / Rfactor Rfree error: 0.02 / Total num. of bins used: 6
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Xplor file |
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Refinement | *PLUS Highest resolution: 2.4 Å | ||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Highest resolution: 2.4 Å |