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Yorodumi- PDB-1trg: E. COLI THYMIDYLATE SYNTHASE IN SYMMETRIC COMPLEX WITH CB3717 AND... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1trg | ||||||
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Title | E. COLI THYMIDYLATE SYNTHASE IN SYMMETRIC COMPLEX WITH CB3717 AND 2'-DEOXYURIDINE 5'-MONOPHOSPHATE (DUMP) | ||||||
Components | THYMIDYLATE SYNTHASE | ||||||
Keywords | METHYLTRANSFERASE / SYMMETRIC TERNARY COMPLEX | ||||||
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 / MOLECULAR REPLACEMENT / Resolution: 1.9 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. #1: Journal: Biochemistry / Year: 1994 Title: Water-Mediated Substrate/Product Discrimination: The Product Complex of Thymidylate Synthase at 1.83 A Authors: Fauman, E.B. / Rutenber, E.E. / Maley, G.F. / Maley, F. / 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. #3: Journal: Biochemistry / Year: 1990 Title: Erratum. 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 | 1trg.cif.gz | 66.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1trg.ent.gz | 52.3 KB | Display | PDB format |
PDBx/mmJSON format | 1trg.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/tr/1trg ftp://data.pdbj.org/pub/pdb/validation_reports/tr/1trg | HTTPS FTP |
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-Related structure data
Related structure data | 1an5C 1aobC 1bduC 1bidC 1dduC 1tduC 1tjsC 1kceS 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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-Components
#1: Protein | Mass: 30543.662 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Cell line: X2913 / Gene: THYA / Plasmid: PTHYA-WT / Gene (production host): THYA / Production host: Escherichia coli (E. coli) / References: UniProt: P0A884, thymidylate synthase |
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#2: Chemical | ChemComp-UMP / |
#3: Chemical | ChemComp-CB3 / |
#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: 2.82 Å3/Da / Density % sol: 52.4 % | |||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | pH: 8 / Details: pH 8.0 | |||||||||||||||||||||||||||||||||||||||||||||
Crystal | *PLUS | |||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS pH: 7.8 / Method: vapor diffusion, hanging drop | |||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 287 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RUH2R / Wavelength: 1.5418 |
Detector | Type: RIGAKU RAXIS IIC / Detector: IMAGE PLATE / Date: Nov 29, 1995 / Details: COLLIMATOR |
Radiation | Monochromator: GRAPHITE(002) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→50 Å / Num. obs: 37807 / % possible obs: 77.4 % / Observed criterion σ(I): 1 / Redundancy: 3.1 % / Biso Wilson estimate: 8.1 Å2 / Rmerge(I) obs: 0.097 / Rsym value: 0.097 / Net I/σ(I): 14.2 |
Reflection shell | Resolution: 1.9→1.98 Å / Redundancy: 1.2 % / Rmerge(I) obs: 0.275 / Mean I/σ(I) obs: 3.1 / Rsym value: 0.321 / % possible all: 45 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: ONE MONOMER OF PDB ENTRY 1KCE Resolution: 1.9→7 Å / Rfactor Rfree error: 0.006 / 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: 20.9 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.9→7 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.9→1.98 Å / Rfactor Rfree error: 0.026 / Total num. of bins used: 8
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Xplor file |
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Software | *PLUS Name: X-PLOR / Version: 3.854 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Rfactor obs: 0.18 / Rfactor Rfree: 0.23 / Rfactor Rwork: 0.18 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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