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Yorodumi- PDB-4psg: Crystal Structure of C.elegans Thymidylate Synthase in complex wi... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4psg | ||||||
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Title | Crystal Structure of C.elegans Thymidylate Synthase in complex with an inhibitor N(4)OHdCMP | ||||||
Components | Thymidylate synthase | ||||||
Keywords | TRANSFERASE/transferase inhibitor / ENZYME / METHYLTRANSFERASE / NUCLEOTIDE BIOSYNTHESIS / PROTEIN DIMER / TRANSFERASE / TRANSFERASE-transferase inhibitor complex | ||||||
Function / homology | Function and homology information thymidylate synthase / thymidylate synthase activity / dTMP biosynthetic process / dTTP biosynthetic process / methylation Similarity search - Function | ||||||
Biological species | Caenorhabditis elegans (invertebrata) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.8 Å | ||||||
Authors | Wilk, P. / Jarmula, A. / Rode, W. | ||||||
Citation | Journal: To be Published Title: Crystal Structure of C.elegans Thymidylate Synthase in complex with an inhibitor N(4)OHdCMP Authors: Dowiercia, A. / Wilk, P. / Rypniewski, W. / Rode, W. / Jarmua, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4psg.cif.gz | 124.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4psg.ent.gz | 97.2 KB | Display | PDB format |
PDBx/mmJSON format | 4psg.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ps/4psg ftp://data.pdbj.org/pub/pdb/validation_reports/ps/4psg | HTTPS FTP |
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-Related structure data
Related structure data | |
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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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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: 0 / Ens-ID: 1 / Beg auth comp-ID: GLN / Beg label comp-ID: GLN / End auth comp-ID: ASP / End label comp-ID: ASP / Refine code: 0 / Auth seq-ID: 24 - 312 / Label seq-ID: 24 - 312
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-Components
#1: Protein | Mass: 35855.902 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Caenorhabditis elegans (invertebrata) / Plasmid: pPIGDM4+stop / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9Y052, thymidylate synthase #2: Chemical | #3: 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: 3.17 Å3/Da / Density % sol: 61.2 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 5.6 Details: 0.1M MES, 0.2M MgAcetate, 15% PEG 8000. Crystals soaked with 36mM inhibitor solution for 80min, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SEALED TUBE / Type: Nova high-flux-micro-focus sealed tube / Wavelength: 1.54056 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Detector: CCD / Date: Jan 23, 2014 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1.54056 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.8→79.804 Å / Num. all: 22154 / Num. obs: 22154 / % possible obs: 99.8 % / Redundancy: 8.7 % / Rsym value: 0.237 / Net I/σ(I): 8.1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Phasing
Phasing | Method: molecular replacement | |||||||||
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Phasing MR | Model details: Phaser MODE: MR_AUTO
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.8→25.11 Å / Cor.coef. Fo:Fc: 0.861 / Cor.coef. Fo:Fc free: 0.834 / WRfactor Rfree: 0.2471 / WRfactor Rwork: 0.2152 / FOM work R set: 0.8384 / SU B: 12.243 / SU ML: 0.249 / SU R Cruickshank DPI: 0.2165 / SU Rfree: 0.0767 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.216 / ESU R Free: 0.077 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES : REFINED INDIVIDUALLY
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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 max: 71.2 Å2 / Biso mean: 16.53 Å2 / Biso min: 2 Å2
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Refinement step | Cycle: LAST / Resolution: 2.8→25.11 Å
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Refine LS restraints |
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Refine LS restraints NCS | Ens-ID: 1 / Number: 346 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.2 Å / Weight position: 0.05
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LS refinement shell | Resolution: 2.8→2.872 Å / Total num. of bins used: 20
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