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Yorodumi- PDB-3fnn: Biochemical and structural analysis of an atypical ThyX: Coryneba... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3fnn | ||||||
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Title | Biochemical and structural analysis of an atypical ThyX: Corynebacterium glutamicum NCHU 87078 depends on ThyA for thymidine biosynthesis | ||||||
Components | Thymidylate synthase thyX | ||||||
Keywords | TRANSFERASE / ThyX / thymidylate synthase / FAD / Flavoprotein / Methyltransferase / Nucleotide biosynthesis | ||||||
Function / homology | Function and homology information thymidylate synthase (FAD) / thymidylate synthase (FAD) activity / dTMP biosynthetic process / dTTP biosynthetic process / flavin adenine dinucleotide binding / methylation Similarity search - Function | ||||||
Biological species | Corynebacterium glutamicum (bacteria) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.3 Å | ||||||
Authors | Wang, W.-C. / Liu, J.-S. / Chang, C.-M. | ||||||
Citation | Journal: To be published Title: Biochemical and structural analysis of an atypical ThyX: Corynebacterium glutamicum NCHU 87078 depends on ThyA for thymidine biosynthesis Authors: Wang, W.-C. / Liu, J.-S. / Chang, C.-M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3fnn.cif.gz | 62.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3fnn.ent.gz | 43.7 KB | Display | PDB format |
PDBx/mmJSON format | 3fnn.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fn/3fnn ftp://data.pdbj.org/pub/pdb/validation_reports/fn/3fnn | HTTPS FTP |
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-Related structure data
Related structure data | 2af6S 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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Components on special symmetry positions |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Dom-ID: 1 / Ens-ID: 1 / Refine code: 1 / Auth asym-ID: A / Label asym-ID: A
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-Components
#1: Protein | Mass: 28928.582 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Corynebacterium glutamicum (bacteria) / Strain: 87078 / Plasmid: PQE30 / Production host: Escherichia coli (E. coli) / References: UniProt: P40111, thymidylate synthase (FAD) |
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#2: Chemical | ChemComp-FAD / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.56 Å3/Da / Density % sol: 52.02 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 123 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å |
Detector | Type: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→30 Å / Num. obs: 13929 / Redundancy: 9.1 % / Rmerge(I) obs: 0.045 |
Reflection shell | Resolution: 2.3→2.38 Å / Redundancy: 6.2 % / Rmerge(I) obs: 0.492 / Mean I/σ(I) obs: 3.61 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2AF6 Resolution: 2.3→27.43 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.927 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 6.614 / SU ML: 0.164 / Cross valid method: THROUGHOUT / ESU R: 0.308 / ESU R Free: 0.232 / Stereochemistry target values: MAXIMUM LIKELIHOOD / 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 / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 47.685 Å2
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Refinement step | Cycle: LAST / Resolution: 2.3→27.43 Å
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Refine LS restraints |
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Refine LS restraints NCS | Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Number: 244 / Refine-ID: X-RAY DIFFRACTION / Rms dev position: 0 Å
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LS refinement shell | Resolution: 2.3→2.359 Å / Total num. of bins used: 20
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