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Yorodumi- PDB-1lcb: LACTOBACILLUS CASEI THYMIDYLATE SYNTHASE TERNARY COMPLEX WITH DTM... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1lcb | ||||||
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Title | LACTOBACILLUS CASEI THYMIDYLATE SYNTHASE TERNARY COMPLEX WITH DTMP AND H2FOLATE | ||||||
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 | 1lcb.cif.gz | 87.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1lcb.ent.gz | 65.4 KB | Display | PDB format |
PDBx/mmJSON format | 1lcb.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/lc/1lcb ftp://data.pdbj.org/pub/pdb/validation_reports/lc/1lcb | 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: ASP 111 - PRO 112 OMEGA = 255.40 PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION 2: LEU 195 - PRO 196 OMEGA = 145.03 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-TMP / |
#3: Chemical | ChemComp-DHF / |
#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: 2.79 Å3/Da / Density % sol: 55.93 % | ||||||||||||||||||||||||||||||||||||
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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 / Detector: IMAGE PLATE / Date: Apr 7, 1994 |
Radiation | Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.48→58.7 Å / Num. obs: 8244 / % possible obs: 51.9 % / Observed criterion σ(I): 1 / Redundancy: 1.512 % / Rmerge(I) obs: 0.196 |
Reflection | *PLUS Rmerge(I) obs: 0.196 |
-Processing
Software |
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Refinement | Resolution: 2.5→15 Å / σ(F): 1.7
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Displacement parameters | Biso mean: 5.5 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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