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Yorodumi- PDB-1lce: LACTOBACILLUS CASEI THYMIDYLATE SYNTHASE TERNARY COMPLEX WITH DUM... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1lce | ||||||
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Title | LACTOBACILLUS CASEI THYMIDYLATE SYNTHASE TERNARY COMPLEX WITH DUMP AND CH2THF | ||||||
Components | THYMIDYLATE SYNTHASE | ||||||
Keywords | TRANSFERASE (METHYLTRANSFERASE) / NUCLEOTIDE SYNTHASE | ||||||
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: 2.5 Å | ||||||
Authors | Birdsall, D.L. / Finer-Moore, J. / Stroud, R.M. | ||||||
Citation | 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 | 1lce.cif.gz | 86.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1lce.ent.gz | 65.9 KB | Display | PDB format |
PDBx/mmJSON format | 1lce.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/lc/1lce ftp://data.pdbj.org/pub/pdb/validation_reports/lc/1lce | 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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Atom site foot note | 1: GLY 98 - PRO 99 OMEGA = 214.26 PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION 2: ASP 111 - PRO 112 OMEGA = 283.81 PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION 3: TYR 307 - PRO 308 OMEGA = 112.96 PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION |
-Components
#1: Protein | Mass: 36630.453 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Lactobacillus casei (bacteria) / References: UniProt: P00469, thymidylate synthase |
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#2: Chemical | ChemComp-UMP / |
#3: Chemical | ChemComp-TMF / |
#4: 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: 2.82 Å3/Da / Density % sol: 56.32 % | ||||||||||||||||||||||||||||||||||||
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Crystal grow | *PLUS pH: 6.8 / Method: vapor diffusion, hanging drop / Details: Hardy, L.W., (1987) Science, 235, 448. | ||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction source | Wavelength: 1.5418 Å |
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Detector | Type: RIGAKU RAXIS / Detector: IMAGE PLATE / Date: Aug 18, 1994 |
Radiation | Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.43→58.8 Å / Num. obs: 9305 / % possible obs: 55 % / Observed criterion σ(I): 1 / Redundancy: 1.818 % / Rmerge(I) obs: 0.098 |
Reflection | *PLUS Rmerge(I) obs: 0.098 |
-Processing
Software |
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Refinement | Resolution: 2.5→15 Å / σ(F): 1.9
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Displacement parameters | Biso mean: 12.9 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.5→15 Å
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Refine LS restraints |
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Software | *PLUS Name: X-PLOR / Version: 3.1 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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