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Yorodumi- PDB-4o7u: Etherocomplex of Enteroccocus faecalis thymidylate synthase with ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4o7u | ||||||
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Title | Etherocomplex of Enteroccocus faecalis thymidylate synthase with 5-hydroxymethilene-6-hydrofolic acid and the phtalimidic inhibitor SS7 | ||||||
Components | Thymidylate synthase | ||||||
Keywords | transferase/transferase inhibitor / transferase / folate binding / transferase-transferase inhibitor complex | ||||||
Function / homology | Function and homology information thymidylate synthase / thymidylate synthase activity / dTMP biosynthetic process / dTTP biosynthetic process / methylation / cytosol Similarity search - Function | ||||||
Biological species | Enterococcus faecalis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å | ||||||
Authors | Mangani, S. / Pozzi, C. | ||||||
Citation | Journal: Eur.J.Med.Chem. / Year: 2016 Title: X-ray crystal structures of Enterococcus faecalis thymidylate synthase with folate binding site inhibitors. Authors: Catalano, A. / Luciani, R. / Carocci, A. / Cortesi, D. / Pozzi, C. / Borsari, C. / Ferrari, S. / Mangani, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4o7u.cif.gz | 246.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4o7u.ent.gz | 200.3 KB | Display | PDB format |
PDBx/mmJSON format | 4o7u.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/o7/4o7u ftp://data.pdbj.org/pub/pdb/validation_reports/o7/4o7u | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
-Protein , 1 types, 4 molecules ABCD
#1: Protein | Mass: 36385.977 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Enterococcus faecalis (bacteria) / Strain: ATCC 700802 / V583 / Gene: thyA, EF_1576 / Production host: Escherichia coli (E. coli) / References: UniProt: Q834R3, thymidylate synthase |
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-Non-polymers , 5 types, 213 molecules
#2: Chemical | ChemComp-SO4 / #3: Chemical | ChemComp-THF / | #4: Chemical | #5: Chemical | ChemComp-SS7 / | #6: 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: 2.25 Å3/Da / Density % sol: 45.39 % |
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Crystal grow | Temperature: 297 K / Method: microbatch under oil / pH: 7 Details: 6.5 mg/mL EfTS, 3.2 M ammonium sulfate, 0.1 M HEPES, co-cystallization with 4 mM SS7 in DMSO in 1/10 SS7/EfTS volume ratio, pH 7.0, microbatch under oil, temperature 297K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.936 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 5, 2009 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.936 Å / Relative weight: 1 |
Reflection | Resolution: 2.4→67.43 Å / Num. all: 38554 / Num. obs: 38554 / % possible obs: 76.5 % / Observed criterion σ(F): 1.4 / Observed criterion σ(I): 2 / Redundancy: 2.4 % / Rmerge(I) obs: 0.124 / Net I/σ(I): 6.5 |
Reflection shell | Resolution: 2.4→2.53 Å / Redundancy: 2.4 % / Rmerge(I) obs: 0.354 / Mean I/σ(I) obs: 3.2 / % possible all: 75.5 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.4→55.67 Å / Cor.coef. Fo:Fc: 0.906 / Cor.coef. Fo:Fc free: 0.83 / SU B: 10.366 / SU ML: 0.241 / Cross valid method: THROUGHOUT / ESU R Free: 0.402 / 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: 15.199 Å2
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Refinement step | Cycle: LAST / Resolution: 2.4→55.67 Å
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Refine LS restraints |
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