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- PDB-1o28: Crystal structure of Thymidylate Synthase Complementing Protein (... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1o28 | ||||||
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Title | Crystal structure of Thymidylate Synthase Complementing Protein (TM0449) from Thermotoga maritima with FdUMP at 2.1 A resolution | ||||||
![]() | Thymidylate synthase thyX | ||||||
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Function / homology | ![]() ![]() ![]() ![]() ![]() ![]() ![]() Similarity search - Function | ||||||
Biological species | ![]() ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Mathews, I.I. / Deacon, A.M. / Canaves, J.M. / McMullan, D. / Lesley, S.A. / Agarwalla, S. / Kuhn, P. / Joint Center for Structural Genomics (JCSG) | ||||||
![]() | ![]() Title: Functional Analysis of Substrate and Cofactor Complex Structures of a Thymidylate Synthase-Complementing Protein Authors: Mathews, I.I. / Deacon, A.M. / Canaves, J.M. / McMullan, D. / Lesley, S.A. / Agarwalla, S. / Kuhn, P. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 200.2 KB | Display | ![]() |
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PDB format | ![]() | 160.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 1o24C ![]() 1o25C ![]() 1o26C ![]() 1o27C ![]() 1o29C ![]() 1o2aC ![]() 1o2bC ![]() 1kq4S C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 27503.680 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() ![]() References: UniProt: Q9WYT0, ![]() #2: Chemical | ChemComp-UFP / ![]() #3: Chemical | ChemComp-EPE / ![]() #4: Chemical | ChemComp-PGE / ![]() #5: Water | ChemComp-HOH / | ![]() |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.06 Å3/Da / Density % sol: 39.72 % | ||||||||||||||||||||||||
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Crystal grow![]() | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 44% PEG 200, 0.1M HEPES, pH 7.5, VAPOR DIFFUSION,HANGING DROP, temperature 295K | ||||||||||||||||||||||||
Crystal grow | *PLUS Method: vapor diffusion, sitting drop / Details: Kuhn, P., (2002) Proteins, 49, 142. | ||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 4r / Detector: CCD / Date: Apr 14, 2002 Details: Flat mirror,single crystal Si(311) bent monochromator |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 2.1→50.746 Å / Num. all: 50458 / Num. obs: 50458 / % possible obs: 95.2 % / Redundancy: 3.2 % / Biso Wilson estimate: 28.461 Å2 / Rsym value: 0.065 / Net I/σ(I): 12.1 |
Reflection shell | Resolution: 2.1→2.15 Å / Redundancy: 2.7 % / Mean I/σ(I) obs: 2.3 / Num. unique all: 3309 / Rsym value: 0.445 / % possible all: 86.3 |
Reflection | *PLUS Highest resolution: 2.1 Å / Lowest resolution: 50.6 Å / Num. measured all: 161945 / Rmerge(I) obs: 0.065 |
Reflection shell | *PLUS % possible obs: 86.3 % / Rmerge(I) obs: 0.445 |
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Processing
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Refinement | Method to determine structure![]() ![]() Starting model: 1KQ4 Resolution: 2.1→20 Å / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: Engh and Huber
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Solvent computation | Solvent model: Bulk solvent correction / Bsol: 0.381386 Å2 / ksol: 55.5185 e/Å3 | ||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 35.8 Å2
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Refine analyze | Luzzati coordinate error obs: 0.2416 Å | ||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.1→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.1→2.11 Å / Total num. of bins used: 49
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Refinement | *PLUS % reflection Rfree: 5 % / Rfactor Rfree![]() ![]() | ||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||
Displacement parameters | *PLUS |