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Open data
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Basic information
Entry | Database: PDB / ID: 1bp0 | ||||||
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Title | THYMIDYLATE SYNTHASE R23I MUTANT | ||||||
![]() | PROTEIN (THYMIDYLATE SYNTHASE) | ||||||
![]() | TRANSFERASE / METHYLTRANSFERASE / NUCLEOTIDE BIOSYNTHESIS | ||||||
Function / homology | ![]() thymidylate synthase / thymidylate synthase activity / dTMP biosynthetic process / dTTP biosynthetic process / methylation / cytosol Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Morse, R. / Finer-Moore, J. / Stroud, R.M. | ||||||
![]() | ![]() Title: Energetic contributions of four arginines to phosphate-binding in thymidylate synthase are more than additive and depend on optimization of "effective charge balance". Authors: Morse, R.J. / Kawase, S. / Santi, D.V. / Finer-Moore, J. / Stroud, R.M. #1: ![]() Title: Stereochemistry of a Multistep/Bipartite Methyl Transfer Reaction: Thymidylate Synthase Authors: Stroud, R.M. / Finer-Moore, J.S. #2: ![]() Title: Refined Structures of Substrate-Bound and Phosphate-Bound Thymidylate Synthase from Lactobacillus Casei Authors: Finer-Moore, J.S. / Fauman, E.B. / Foster, P.G. / Perry, K.M. / Santi, D.V. / Stroud, R.M. #3: ![]() Title: Atomic Structure of Thymidylate Synthase: Target for Rational Drug Design Authors: Hardy, L.W. / Finer-Moore, J.S. / Montfort, W.R. / Jones, M.O. / Santi, D.V. / Stroud, R.M. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 80.7 KB | Display | ![]() |
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PDB format | ![]() | 59.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 1bo7C ![]() 1bo8C ![]() 1bp6C ![]() 1bpjC ![]() 1tdm S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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Unit cell |
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Components on special symmetry positions |
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Components
#1: Protein | Mass: 36586.418 Da / Num. of mol.: 1 / Mutation: R23I Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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#2: Chemical | ChemComp-K / |
#3: Chemical | ChemComp-UMP / |
#4: Water | ChemComp-HOH / |
Nonpolymer details | K A 52 IS A POSSIBLE POTASSIUM ION THAT LIES ON A MOLECULAR AND CRYSTALLOG |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3 Å3/Da / Density % sol: 57 % | ||||||||||||||||||||||||||||||
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Crystal grow | pH: 7 / Details: pH 7.0 | ||||||||||||||||||||||||||||||
Crystal grow | *PLUS Method: vapor diffusion / Details: Finer-Moore, J.S., (1993) J.Mol.Biol., 232, 1101. | ||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 293 K |
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Diffraction source | Source: ![]() |
Detector | Type: RIGAKU RAXIS IIC / Detector: IMAGE PLATE |
Radiation | Monochromator: GRAPHITE MONOCHROMETER / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.4→50 Å / Num. obs: 16217 / % possible obs: 87.6 % / Observed criterion σ(I): 0 / Redundancy: 3.7 % / Biso Wilson estimate: 34.2 Å2 / Rmerge(I) obs: 0.084 / Rsym value: 8.4 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1TDM ![]() 1tdm Resolution: 2.4→7 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 10000 / Data cutoff low absF: 0.001 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
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Displacement parameters | Biso mean: 34.3 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.4→7 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.4→2.5 Å / Rfactor Rfree error: 0.025 / Total num. of bins used: 8
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Xplor file |
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Software | *PLUS Name: ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Rfactor obs: 0.195 / Rfactor Rfree: 0.256 / Rfactor Rwork: 0.195 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS Biso mean: 34 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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