+Open data
-Basic information
Entry | Database: PDB / ID: 1bo7 | ||||||
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Title | THYMIDYLATE SYNTHASE R179T MUTANT | ||||||
Components | PROTEIN (THYMIDYLATE SYNTHASE) | ||||||
Keywords | TRANSFERASE / TRANSFERASE (METHYLTRANSFERASE) / METHYLTRANSFERASE / NUCLEOTIDE BIOSYNTHESIS | ||||||
Function / homology | Function and homology information thymidylate synthase / thymidylate synthase activity / dTMP biosynthetic process / dTTP biosynthetic process / methylation / cytoplasm Similarity search - Function | ||||||
Biological species | Lactobacillus casei (bacteria) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.4 Å | ||||||
Authors | Morse, R. / Finer-Moore, J. / Stroud, R.M. | ||||||
Citation | Journal: Biochemistry / Year: 2000 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: Journal: Faseb J. / Year: 1993 Title: Stereochemistry of a Multistep/Bipartite Methyl Transfer Reaction: Thymidylate Synthase Authors: Stroud, R.M. / Finer-Moore, J.S. #2: Journal: J.Mol.Biol. / Year: 1993 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: Journal: Science / Year: 1987 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1bo7.cif.gz | 80.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1bo7.ent.gz | 59.6 KB | Display | PDB format |
PDBx/mmJSON format | 1bo7.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bo/1bo7 ftp://data.pdbj.org/pub/pdb/validation_reports/bo/1bo7 | HTTPS FTP |
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-Related structure data
Related structure data | 1bo8C 1bp0C 1bp6C 1bpjC 1tdm S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-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: 36574.363 Da / Num. of mol.: 1 / Mutation: R179T Source method: isolated from a genetically manipulated source Source: (gene. exp.) Lactobacillus casei (bacteria) / Strain: E. COLI CHI-2913 / Description: SYNTHETIC GENE / Plasmid: PKPTSD / Production host: Escherichia coli (E. coli) / Strain (production host): CHI-2913 / References: UniProt: P00469, thymidylate synthase |
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#2: Chemical | ChemComp-U / |
#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: 2.94 Å3/Da / Density % sol: 57 % | ||||||||||||||||||||||||||||||
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Crystal grow | pH: 7 / Details: pH 7.0 | ||||||||||||||||||||||||||||||
Crystal grow | *PLUS Method: vapor diffusion | ||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 293 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.5418 |
Detector | Type: SIEMENS / Detector: AREA DETECTOR / Date: Apr 15, 1995 |
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: 17548 / % possible obs: 96.2 % / Observed criterion σ(I): 0 / Redundancy: 3.6 % / Biso Wilson estimate: 42.1 Å2 / Rmerge(I) obs: 0.074 / Rsym value: 7.4 / Net I/σ(I): 14.9 |
Reflection shell | Resolution: 2.4→2.5 Å / Redundancy: 3.5 % / Mean I/σ(I) obs: 2 / % possible all: 91.7 |
Reflection shell | *PLUS % possible obs: 91.7 % |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1TDM 1tdm Resolution: 2.4→7 Å / Rfactor Rfree error: 0.008 / Data cutoff high absF: 10000 / Data cutoff low absF: 0.001 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2
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Displacement parameters | Biso mean: 38.2 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: 0.026 / Total num. of bins used: 8
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Xplor file |
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Software | *PLUS Name: X-PLOR / Version: 3.8 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Rfactor obs: 0.205 / Rfactor Rfree: 0.251 / Rfactor Rwork: 0.205 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS Biso mean: 38 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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