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- PDB-1o2b: Crystal structure of Thymidylate Synthase Complementing Protein (... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1o2b | ||||||
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Title | Crystal structure of Thymidylate Synthase Complementing Protein (TM0449) from Thermotoga maritima with FAD and PO4 at 2.45 A resolution | ||||||
![]() | Thymidylate synthase thyX | ||||||
![]() | TRANSFERASE / TM0449 / THYMIDYLATE SYNTHASE COMPLEMENTING PROTEIN / STRUCTURAL GENOMICS / JCSG / Joint Center for Structural Genomics / PSI / Protein Structure Initiative | ||||||
Function / homology | ![]() thymidylate synthase (FAD) / thymidylate synthase (FAD) activity / thymidylate synthase activity / dTMP biosynthetic process / dTTP biosynthetic process / NADPH binding / flavin adenine dinucleotide binding / methylation 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 | ![]() | 197.8 KB | Display | ![]() |
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PDB format | ![]() | 158.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.6 MB | Display | ![]() |
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Full document | ![]() | 1.6 MB | Display | |
Data in XML | ![]() | 39.4 KB | Display | |
Data in CIF | ![]() | 51.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1o24C ![]() 1o25C ![]() 1o26C ![]() 1o27C ![]() 1o28C ![]() 1o29C ![]() 1o2aC ![]() 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, Transferases; Transferring one-carbon groups; Methyltransferases #2: Chemical | #3: Chemical | ChemComp-FAD / #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.22 Å3/Da / Density % sol: 44.11 % | ||||||||||||||||||||||||
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 45 PEG 200, 0.1M HEPES, pH 7.5, 8mM sodium, 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: Mar 24, 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: 0.94641 Å / Relative weight: 1 |
Reflection | Resolution: 2.45→47.16 Å / Num. all: 33811 / Num. obs: 33811 / % possible obs: 95 % / Redundancy: 2.9 % / Biso Wilson estimate: 46.811 Å2 / Rsym value: 0.081 / Net I/σ(I): 10.1 |
Reflection shell | Resolution: 2.45→2.51 Å / Redundancy: 2.1 % / Mean I/σ(I) obs: 1.4 / Num. unique all: 2015 / Rsym value: 0.66 / % possible all: 77.9 |
Reflection | *PLUS Highest resolution: 2.5 Å / Lowest resolution: 47.1 Å / Num. obs: 32278 / % possible obs: 96.2 % / Num. measured all: 96569 / Rmerge(I) obs: 0.08 |
Reflection shell | *PLUS % possible obs: 87.3 % / Rmerge(I) obs: 0.469 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1KQ4 Resolution: 2.45→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: 0.348113 Å2 / ksol: 52.0584 e/Å3 | ||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 50.9 Å2
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Refine analyze | Luzzati coordinate error obs: 0.3118 Å | ||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.45→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.45→2.48 Å / Total num. of bins used: 32
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Refinement | *PLUS Highest resolution: 2.5 Å / Lowest resolution: 20 Å / Num. reflection obs: 32148 / Num. reflection Rfree: 1559 / Rfactor Rfree: 0.261 / Rfactor Rwork: 0.201 / % reflection Rfree: 5 % | ||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||
Displacement parameters | *PLUS |