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Yorodumi- PDB-1njd: THYMIDYLATE SYNTHASE, MUTATION, N229D WITH 2'-DEOXYURIDINE 5'-MON... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1njd | ||||||
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Title | THYMIDYLATE SYNTHASE, MUTATION, N229D WITH 2'-DEOXYURIDINE 5'-MONOPHOSPHATE (DUMP) | ||||||
Components | THYMIDYLATE SYNTHASE | ||||||
Keywords | TRANSFERASE (METHYLTRANSFERASE) / TRANSFERASE / 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 / Resolution: 2.2 Å | ||||||
Authors | Finer-Moore, J. / Stroud, R.M. | ||||||
Citation | Journal: Biochemistry / Year: 1996 Title: Partitioning roles of side chains in affinity, orientation, and catalysis with structures for mutant complexes: asparagine-229 in thymidylate synthase. Authors: Finer-Moore, J.S. / Liu, L. / Schafmeister, C.E. / Birdsall, D.L. / Mau, T. / Santi, D.V. / 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. / Fauman, E.B. / Foster, P.G. / Perry, K.M. / Santi, D.V. / Stroud, R.M. #3: Journal: Biochemistry / Year: 1993 Title: Exclusion of 2'-Deoxycytidine 5'-Monophosphate by Asparagine 229 of Thymidylate Synthase Authors: Liu, L. / Santi, D.V. #4: Journal: Biochemistry / Year: 1992 Title: Mutation of Asparagine 229 to Aspartate in Thymidylate Synthase Converts the Enzyme to a Deoxycytidylate Methylase Authors: Liu, L. / Santi, D.V. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1njd.cif.gz | 77.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1njd.ent.gz | 58.8 KB | Display | PDB format |
PDBx/mmJSON format | 1njd.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/nj/1njd ftp://data.pdbj.org/pub/pdb/validation_reports/nj/1njd | 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 on special symmetry positions |
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-Components
#1: Protein | Mass: 36631.438 Da / Num. of mol.: 1 / Mutation: N229D Source method: isolated from a genetically manipulated source Source: (gene. exp.) Lactobacillus casei (bacteria) / Description: PURCHASED FROM SIGMA / Gene: N229D MUTANT OF CLONED L. CASE / Plasmid: PKPTSD / Gene (production host): N229D MUTANT OF CLONED L. CASEI TS / Production host: Escherichia coli (E. coli) Strain (production host): STRAIN CHI-2913 (WHICH LACKS A THYMIDYLATE SYNTHASE GENE) References: UniProt: P00469, thymidylate synthase |
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#2: Chemical | ChemComp-UMP / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.93 Å3/Da / Density % sol: 55 % | |||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | pH: 7.4 / Details: pH 7.4 | |||||||||||||||||||||||||||||||||||||||||||||
Crystal | *PLUS | |||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS pH: 7 / 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 / Detector: IMAGE PLATE / Date: Apr 1, 1993 |
Radiation | Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→50 Å / Num. obs: 13487 / % possible obs: 57 % / Observed criterion σ(I): 1 / Redundancy: 3 % / Rmerge(I) obs: 0.097 |
Reflection | *PLUS Num. measured all: 37757 |
-Processing
Software |
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Refinement | Resolution: 2.2→50 Å / σ(F): 1
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Displacement parameters | Biso mean: 22.5 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.2→50 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 Lowest resolution: 8 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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