+Open data
-Basic information
Entry | Database: PDB / ID: 1iim | ||||||
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Title | thymidylyltransferase complexed with TTP | ||||||
Components | glucose-1-phosphate thymidylyltransferase | ||||||
Keywords | TRANSFERASE | ||||||
Function / homology | Function and homology information glucose-1-phosphate thymidylyltransferase / glucose-1-phosphate thymidylyltransferase activity / O antigen biosynthetic process / dTDP-rhamnose biosynthetic process / extracellular polysaccharide biosynthetic process / magnesium ion binding / metal ion binding Similarity search - Function | ||||||
Biological species | Salmonella enterica (bacteria) | ||||||
Method | X-RAY DIFFRACTION / Resolution: 2.1 Å | ||||||
Authors | Barton, W.A. / Lesniak, J. / Biggins, J.B. / Jeffrey, P.D. / Jiang, J. / Rajashankar, K.R. / Thorson, J.S. / Nikolov, D.B. | ||||||
Citation | Journal: Nat.Struct.Biol. / Year: 2001 Title: Structure, mechanism and engineering of a nucleotidylyltransferase as a first step toward glycorandomization. Authors: Barton, W.A. / Lesniak, J. / Biggins, J.B. / Jeffrey, P.D. / Jiang, J. / Rajashankar, K.R. / Thorson, J.S. / Nikolov, D.B. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1iim.cif.gz | 135.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1iim.ent.gz | 106.1 KB | Display | PDB format |
PDBx/mmJSON format | 1iim.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ii/1iim ftp://data.pdbj.org/pub/pdb/validation_reports/ii/1iim | 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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Details | The second part of the biological assembly is generated by the two fold axis: -x -y -z+1/2 |
-Components
#1: Protein | Mass: 32485.201 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Salmonella enterica (bacteria) / Strain: LT2 / Plasmid: pET22 / Production host: Escherichia coli (E. coli) / Strain (production host): JM109 References: UniProt: Q9F7K6, UniProt: P26393*PLUS, glucose-1-phosphate thymidylyltransferase #2: Chemical | ChemComp-TTP / #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.62 Å3/Da / Density % sol: 53 % | ||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: Tris, Mono-ammonium dihydrogen phosphate, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K | ||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS pH: 7.2 | ||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 120 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 |
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Details: mirrors |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.01→19.26 Å / Num. all: 45400 / Observed criterion σ(F): 0 / Biso Wilson estimate: 18.8 Å2 / Limit h max: 59 / Limit h min: 0 / Limit k max: 40 / Limit k min: 0 / Limit l max: 46 / Limit l min: 0 / Observed criterion F max: 299778.95 / Observed criterion F min: 0.32 |
Reflection | *PLUS % possible obs: 98.2 % / Redundancy: 9 % / Rmerge(I) obs: 0.109 |
-Processing
Software |
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Refinement | Resolution: 2.1→19.26 Å / Rfactor Rfree error: 0.003 / Occupancy max: 1 / Occupancy min: 1 / Cross valid method: THROUGHOUT Details: There are three C-terminal residues in the crystal for which the author does not see clear density: LYS 290, GLY 291, LEU 292. There is no density beyond the CB for LYS 154.
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Solvent computation | Solvent model: CNS bulk solvent model used / Bsol: 52.2732 Å2 / ksol: 0.369264 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 59.32 Å2 / Biso mean: 23.92 Å2 / Biso min: 8.81 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.1→19.26 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION
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Xplor file |
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Software | *PLUS Name: CNS / Version: 1 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Lowest resolution: 8 Å / Num. reflection obs: 45403 / Num. reflection Rfree: 3583 / % reflection Rfree: 10 % / Rfactor obs: 0.198 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor Rfree: 0.269 / % reflection Rfree: 8.8 % / Rfactor Rwork: 0.268 |