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Yorodumi- PDB-1tdu: E. COLI THYMIDYLATE SYNTHASE IN COMPLEX WITH CB3717 AND 2'-DEOXYU... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1tdu | ||||||
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Title | E. COLI THYMIDYLATE SYNTHASE IN COMPLEX WITH CB3717 AND 2'-DEOXYURIDINE (DURD) | ||||||
Components | THYMIDYLATE SYNTHASE | ||||||
Keywords | METHYLTRANSFERASE / TRANSFERASE (METHYLTRANSFERASE) / SUBSTRATE MODULES | ||||||
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) | ||||||
Method | X-RAY DIFFRACTION / DIFFERENCE FOURIER / Resolution: 2.1 Å | ||||||
Authors | Stout, T.J. / Sage, C.R. / Stroud, R.M. | ||||||
Citation | Journal: Structure / Year: 1998 Title: The additivity of substrate fragments in enzyme-ligand binding. Authors: Stout, T.J. / Sage, C.R. / 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 | 1tdu.cif.gz | 118 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1tdu.ent.gz | 96.3 KB | Display | PDB format |
PDBx/mmJSON format | 1tdu.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1tdu_validation.pdf.gz | 550.3 KB | Display | wwPDB validaton report |
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Full document | 1tdu_full_validation.pdf.gz | 568.5 KB | Display | |
Data in XML | 1tdu_validation.xml.gz | 14.9 KB | Display | |
Data in CIF | 1tdu_validation.cif.gz | 21.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/td/1tdu ftp://data.pdbj.org/pub/pdb/validation_reports/td/1tdu | HTTPS FTP |
-Related structure data
Related structure data | 1an5C 1aobC 1bduC 1bidC 1dduC 1tjsC 1trgC 1zprS S: Starting model for refinement C: citing same article (ref.) |
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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 oper: (Code: given Matrix: (-1, 0.01, -0.009), Vector: |
-Components
#1: Protein | Mass: 30543.662 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Cell line: CHI-2913 / Gene: THYA / Plasmid: PTHYA-WT / Cell line (production host): CHI-2913 / Gene (production host): THYA / Production host: Escherichia coli (E. coli) / References: UniProt: P0A884, thymidylate synthase #2: Chemical | #3: Chemical | #4: Chemical | #5: 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: 2.56 Å3/Da / Density % sol: 52.4 % | |||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Method: vapor diffusion, hanging drop / pH: 7.8 Details: CRYSTALLIZATION WAS CONDUCTED IN HANGING DROPS CONTAINING 4.2 MG/ML E. COLI TS, 0.38 MM DURD, 3.8 MM DTT, 1.0 MM CB3717 AND 1.2 M (NH4)2SO4, PH 7.8 (20 MM KPO4) OVER A WELL SOLUTION ...Details: CRYSTALLIZATION WAS CONDUCTED IN HANGING DROPS CONTAINING 4.2 MG/ML E. COLI TS, 0.38 MM DURD, 3.8 MM DTT, 1.0 MM CB3717 AND 1.2 M (NH4)2SO4, PH 7.8 (20 MM KPO4) OVER A WELL SOLUTION CONTAINING 2.4 M (NH4)2SO4 AND 1.0 MM DTT., vapor diffusion - hanging drop | |||||||||||||||||||||||||||||||||||||||||||||
Crystal | *PLUS | |||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Method: vapor diffusion, hanging drop | |||||||||||||||||||||||||||||||||||||||||||||
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 RUH2R / Wavelength: 1.5418 |
Detector | Type: RIGAKU / Detector: IMAGE PLATE / Date: Nov 1, 1996 |
Radiation | Monochromator: GRAPHITE(002) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→50 Å / Num. obs: 36809 / % possible obs: 95.2 % / Observed criterion σ(I): 0 / Redundancy: 4.8 % / Biso Wilson estimate: 17.6 Å2 / Rmerge(I) obs: 0.064 / Rsym value: 0.064 / Net I/σ(I): 15.9 |
Reflection shell | Resolution: 2.1→2.16 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.278 / Mean I/σ(I) obs: 3.6 / Rsym value: 0.278 / % possible all: 90.2 |
Reflection | *PLUS Num. measured all: 148364 |
-Processing
Software |
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Refinement | Method to determine structure: DIFFERENCE FOURIER Starting model: PDB ENTRY 1ZPR Resolution: 2.1→8 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 10000000 / Data cutoff low absF: 0.001 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2
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Displacement parameters | Biso mean: 25.5 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.1→8 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.1→2.23 Å / Rfactor Rfree error: 0.019 / Total num. of bins used: 6
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Xplor file |
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Software | *PLUS Name: X-PLOR / Version: 3.843 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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