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Yorodumi- PDB-5ioq: Flavin-dependent thymidylate synthase in complex with FAD and deo... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5ioq | ||||||||||||
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Title | Flavin-dependent thymidylate synthase in complex with FAD and deoxyuridine | ||||||||||||
Components | Thymidylate synthase ThyX | ||||||||||||
Keywords | TRANSFERASE / FAD-dependent / nucleotide biosynthesis / reductive methylation | ||||||||||||
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: 1.93 Å | ||||||||||||
Authors | Bernard, S.M. / Stull, F.W. / Smith, J.L. | ||||||||||||
Funding support | United States, 3items
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Citation | Journal: Biochemistry / Year: 2016 Title: Deprotonations in the Reaction of Flavin-Dependent Thymidylate Synthase. Authors: Stull, F.W. / Bernard, S.M. / Sapra, A. / Smith, J.L. / Zuiderweg, E.R. / Palfey, B.A. | ||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5ioq.cif.gz | 202.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5ioq.ent.gz | 160.9 KB | Display | PDB format |
PDBx/mmJSON format | 5ioq.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/io/5ioq ftp://data.pdbj.org/pub/pdb/validation_reports/io/5ioq | HTTPS FTP |
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-Related structure data
Related structure data | 5iorC 5iosC 5iotC 4gt9S 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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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: 0 / Refine code: 0
NCS ensembles :
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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 (strain ATCC 43589 / MSB8 / DSM 3109 / JCM 10099) (bacteria) Strain: ATCC 43589 / MSB8 / DSM 3109 / JCM 10099 / Gene: thyX, thy1, TM_0449 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9WYT0, thymidylate synthase (FAD) #2: Chemical | ChemComp-FAD / #3: Chemical | ChemComp-PGE / #4: Chemical | ChemComp-DUR / #5: 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: 39.37 % |
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Crystal grow | Temperature: 293.15 K / Method: vapor diffusion / pH: 8 Details: 40-50% PEG 200, 0-150 mM NaCl, 100 mM Tris-HCl pH 8.0 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.033 Å |
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jun 6, 2013 |
Radiation | Monochromator: double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.033 Å / Relative weight: 1 |
Reflection | Resolution: 1.93→89.86 Å / Num. obs: 67137 / % possible obs: 98.1 % / Redundancy: 7.6 % / Rsym value: 0.094 / Net I/σ(I): 22.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4GT9 Resolution: 1.93→89.86 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.956 / SU B: 3.598 / SU ML: 0.101 / Cross valid method: THROUGHOUT / ESU R: 0.168 / ESU R Free: 0.141 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 39.126 Å2
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Refinement step | Cycle: 1 / Resolution: 1.93→89.86 Å
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Refine LS restraints |
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