[English] 日本語
Yorodumi- PDB-1o28: Crystal structure of Thymidylate Synthase Complementing Protein (... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1o28 | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of Thymidylate Synthase Complementing Protein (TM0449) from Thermotoga maritima with FdUMP at 2.1 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: 2.1 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 |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 1o28.cif.gz | 200.2 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb1o28.ent.gz | 160.8 KB | Display | PDB format |
PDBx/mmJSON format | 1o28.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/o2/1o28 ftp://data.pdbj.org/pub/pdb/validation_reports/o2/1o28 | HTTPS FTP |
---|
-Related structure data
Related structure data | 1o24C 1o25C 1o26C 1o27C 1o29C 1o2aC 1o2bC 1kq4S C: citing same article (ref.) S: Starting model for refinement |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-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-EPE / #4: Chemical | ChemComp-PGE / #5: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.06 Å3/Da / Density % sol: 39.72 % | ||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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
|
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL9-1 / Wavelength: 0.98039 |
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: 0.98039 Å / Relative weight: 1 |
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 |
-Processing
Software |
| ||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT 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
| ||||||||||||||||||||||||||||
Solvent computation | Solvent model: Bulk solvent correction / Bsol: 0.381386 Å2 / ksol: 55.5185 e/Å3 | ||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 35.8 Å2
| ||||||||||||||||||||||||||||
Refine analyze | Luzzati coordinate error obs: 0.2416 Å | ||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.1→20 Å
| ||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.1→2.11 Å / Total num. of bins used: 49
| ||||||||||||||||||||||||||||
Refinement | *PLUS % reflection Rfree: 5 % / Rfactor Rfree: 0.24 / Rfactor Rwork: 0.193 | ||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||
Displacement parameters | *PLUS |