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Yorodumi- PDB-1o29: Crystal structure of Thymidylate Synthase Complementing Protein (... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1o29 | ||||||
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Title | Crystal structure of Thymidylate Synthase Complementing Protein (TM0449) from Thermotoga maritima with FAD and FdUMP at 2.0 A resolution | ||||||
Components | Thymidylate synthase thyX | ||||||
Keywords | TRANSFERASE / TM0449 / THYMIDYLATE SYNTHASE COMPLEMENTING PROTEIN / STRUCTURAL GENOMICS / JCSG / Joint Center for Structural Genomics / PSI / Protein Structure Initiative | ||||||
Function / homology | Function and homology information 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 | Thermotoga maritima (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å | ||||||
Authors | Mathews, I.I. / Deacon, A.M. / Canaves, J.M. / McMullan, D. / Lesley, S.A. / Agarwalla, S. / Kuhn, P. / Joint Center for Structural Genomics (JCSG) | ||||||
Citation | Journal: Structure / Year: 2003 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1o29.cif.gz | 206 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1o29.ent.gz | 166 KB | Display | PDB format |
PDBx/mmJSON format | 1o29.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/o2/1o29 ftp://data.pdbj.org/pub/pdb/validation_reports/o2/1o29 | HTTPS FTP |
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-Related structure data
Related structure data | 1o24C 1o25C 1o26C 1o27C 1o28C 1o2aC 1o2bC 1kq4S C: citing same article (ref.) S: Starting model for refinement |
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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: 27503.680 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thermotoga maritima (bacteria) / Gene: TM0449 / Production host: Escherichia coli (E. coli) References: UniProt: Q9WYT0, Transferases; Transferring one-carbon groups; Methyltransferases #2: Chemical | ChemComp-UFP / #3: Chemical | ChemComp-FAD / #4: 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: 2.03 Å3/Da / Density % sol: 38.82 % | ||||||||||||||||||||||||
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 8 Details: 47% PEG 200, 0.1M Tris-HCL, pH 8.0, VAPOR DIFFUSION,HANGING DROP, temperature 295K | ||||||||||||||||||||||||
Crystal grow | *PLUS pH: 7.5 / 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: SYNCHROTRON / Site: SSRL / Beamline: BL9-1 / Wavelength: 0.91984 |
Detector | Type: ADSC QUANTUM 4r / Detector: CCD / Date: Apr 22, 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: 0.91984 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→45.129 Å / Num. all: 71914 / Num. obs: 71914 / % possible obs: 99.2 % / Redundancy: 4.2 % / Biso Wilson estimate: 24.902 Å2 / Rsym value: 0.075 / Net I/σ(I): 14 |
Reflection shell | Resolution: 1.9→1.95 Å / Redundancy: 4.1 % / Mean I/σ(I) obs: 1.8 / Num. unique all: 5117 / Rsym value: 0.75 / % possible all: 96.6 |
Reflection | *PLUS Highest resolution: 2 Å / Lowest resolution: 45.2 Å / Num. obs: 62119 / % possible obs: 99.6 % / Num. measured all: 264891 / Rmerge(I) obs: 0.068 |
Reflection shell | *PLUS % possible obs: 98 % / Rmerge(I) obs: 0.429 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1KQ4 Resolution: 2→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: 0.364627 Å2 / ksol: 43.3112 e/Å3 | ||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 30 Å2
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Refine analyze | Luzzati coordinate error obs: 0.2276 Å | ||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2→2.01 Å / Total num. of bins used: 50
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Refinement | *PLUS Lowest resolution: 20 Å / % reflection Rfree: 5 % / Rfactor Rfree: 0.232 / Rfactor Rwork: 0.194 | ||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||
Displacement parameters | *PLUS |