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Yorodumi- PDB-3bz0: Lactobacillus Casei Thymidylate Synthase Ternary Complex with DUM... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3bz0 | ||||||
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Title | Lactobacillus Casei Thymidylate Synthase Ternary Complex with DUMP and the Phtalimidic Derivative C00 | ||||||
Components | Thymidylate synthase | ||||||
Keywords | TRANSFERASE / NUCLEOTIDE SYNTHASE / STRUCTURE BASED DRUG DESIGN / 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 / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å | ||||||
Authors | Leone, R. / Cancian, L. / Costi, M.P. / Ferrari, S. / Luciani, R. / Mangani, S. | ||||||
Citation | Journal: J.Med.Chem. / Year: 2011 Title: Identification of the binding modes of N-phenylphthalimides inhibiting bacterial thymidylate synthase through X-ray crystallography screening Authors: Mangani, S. / Cancian, L. / Leone, R. / Pozzi, C. / Lazzari, S. / Luciani, R. / Ferrari, S. / Costi, M.P. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3bz0.cif.gz | 78.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3bz0.ent.gz | 58 KB | Display | PDB format |
PDBx/mmJSON format | 3bz0.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bz/3bz0 ftp://data.pdbj.org/pub/pdb/validation_reports/bz/3bz0 | HTTPS FTP |
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-Related structure data
Related structure data | 3bnzC 3byxC 3c06C 3c0aC 3ijzC 3ik0C 3ik1C 1lcaS C: citing same article (ref.) 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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Components on special symmetry positions |
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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) / 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: Chemical | ChemComp-C00 / |
#4: 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: 2.68 Å3/Da / Density % sol: 54.13 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.4 Details: 1mM EDTA, 20 mM Tris-HCl, dUMP, 100mM ammonium phopshate, 5% (v/v) PEG 400, pH 7.4, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: BW7B / Wavelength: 1.078 Å |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jan 1, 2005 |
Radiation | Monochromator: Si [111] / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.078 Å / Relative weight: 1 |
Reflection | Resolution: 2.7→33.37 Å / Num. all: 10447 / Num. obs: 10443 / % possible obs: 88.6 % / Observed criterion σ(I): 1.7 / Redundancy: 4 % / Biso Wilson estimate: 56.53 Å2 / Rmerge(I) obs: 0.139 / Rsym value: 0.139 / Net I/σ(I): 4.3 |
Reflection shell | Resolution: 2.7→2.85 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.439 / Mean I/σ(I) obs: 1.7 / Num. unique all: 1502 / Rsym value: 0.439 / % possible all: 92.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1LCA Resolution: 2.7→33.37 Å / Cor.coef. Fo:Fc: 0.907 / Cor.coef. Fo:Fc free: 0.801 / SU B: 15.15 / SU ML: 0.32 / Cross valid method: THROUGHOUT / ESU R Free: 0.475 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 37.422 Å2
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Refine analyze | Luzzati coordinate error free: 0.475 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.7→33.37 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.7→2.77 Å / Total num. of bins used: 20
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