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Yorodumi- PDB-1vzd: L. CASEI THYMIDYLATE SYNTHASE MUTANT E60Q TERNARY COMPLEX WITH FD... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1vzd | ||||||
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Title | L. CASEI THYMIDYLATE SYNTHASE MUTANT E60Q TERNARY COMPLEX WITH FDUMP AND CB3717 | ||||||
Components | THYMIDYLATE SYNTHASE | ||||||
Keywords | METHYLTRANSFERASE / NUCLEOTIDE SYNTHASE | ||||||
Function / homology | Function and homology information thymidylate synthase / thymidylate synthase activity / dTMP biosynthetic process / dTTP biosynthetic process / methylation / cytosol Similarity search - Function | ||||||
Biological species | Lactobacillus casei (bacteria) | ||||||
Method | X-RAY DIFFRACTION / Resolution: 2.5 Å | ||||||
Authors | Birdsall, D.L. / Finer-Moore, J. / Stroud, R.M. | ||||||
Citation | Journal: Protein Eng. / Year: 1998 Title: The separate effects of E60Q in Lactobacillus casei thymidylate synthase delineate between mechanisms for formation of intermediates in catalysis. Authors: Birdsall, D.L. / Huang, W. / Santi, D.V. / Stroud, R.M. / Finer-Moore, J. #1: Journal: J.Mol.Biol. / Year: 1993 Title: Refined Structures of Substrate-Bound and Phosphate-Bound Thymidylate Synthase from Lactobacillus Casei Authors: Finer-Moore, J. / Fauman, E.B. / Foster, P.G. / Perry, K.M. / Santi, D.V. / Stroud, R.M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1vzd.cif.gz | 98.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1vzd.ent.gz | 75.1 KB | Display | PDB format |
PDBx/mmJSON format | 1vzd.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vz/1vzd ftp://data.pdbj.org/pub/pdb/validation_reports/vz/1vzd | HTTPS FTP |
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-Related 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: 36585.461 Da / Num. of mol.: 1 / Mutation: E60Q Source method: isolated from a genetically manipulated source Source: (gene. exp.) Lactobacillus casei (bacteria) / Gene: THYMIDYLATE SYNTHASE / Plasmid: PSCTS13 / Gene (production host): THYMIDYLATE SYNTHASE / Production host: Escherichia coli (E. coli) / Strain (production host): X(CHI)2913 THY- / References: UniProt: P00469, thymidylate synthase |
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#2: Chemical | ChemComp-UFP / |
#3: Chemical | ChemComp-CB3 / |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.8 Å3/Da / Density % sol: 56.1 % | ||||||||||||||||||||||||||||||
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Crystal grow | *PLUS pH: 6.8 / Method: vapor diffusion | ||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction source | Wavelength: 1.5418 |
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Detector | Type: RIGAKU RAXIS IIC / Detector: IMAGE PLATE / Date: Apr 5, 1994 |
Radiation | Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Num. obs: 10269 / % possible obs: 45.5 % / Observed criterion σ(I): 1 / Rmerge(I) obs: 0.1154 |
Reflection | *PLUS Highest resolution: 2.5 Å / Lowest resolution: 15 Å / % possible obs: 60.7 % |
-Processing
Software |
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Refinement | Resolution: 2.5→15 Å / σ(F): 1 /
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Displacement parameters | Biso mean: 10.6 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.5→15 Å
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Refine LS restraints |
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Xplor file |
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Software | *PLUS Name: X-PLOR / Version: 3.1 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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