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- PDB-1l4e: The crystal structure of CobT complexed with alpha-ribazole-5'-ph... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1l4e | ||||||
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Title | The crystal structure of CobT complexed with alpha-ribazole-5'-phosphate | ||||||
![]() | Nicotinate-nucleotide--dimethylbenzimidazole phosphoribosyltransferase | ||||||
![]() | TRANSFERASE / CobT / cobalamin synthetic enzyme / phosphoribosyltransferase / 5 / 6-dimethylbenzimidazole / nicotinate mononucleotide | ||||||
Function / homology | ![]() nicotinate-nucleotide-dimethylbenzimidazole phosphoribosyltransferase / nicotinate-nucleotide-dimethylbenzimidazole phosphoribosyltransferase activity / cobalamin biosynthetic process / nucleotide binding Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Cheong, C.-G. / Escalante-Semerena, J. / Rayment, I. | ||||||
![]() | ![]() Title: Capture of a labile substrate by expulsion of water molecules from the active site of nicotinate mononucleotide:5,6-dimethylbenzimidazole phosphoribosyltransferase (CobT) from Salmonella enterica. Authors: Cheong, C.G. / Escalante-Semerena, J.C. / Rayment, I. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 76.8 KB | Display | ![]() |
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PDB format | ![]() | 55.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 772 KB | Display | ![]() |
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Full document | ![]() | 775 KB | Display | |
Data in XML | ![]() | 15.2 KB | Display | |
Data in CIF | ![]() | 21.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1l4bC ![]() 1l4fC ![]() 1l4gC ![]() 1l4hC ![]() 1l4kC ![]() 1l4lC ![]() 1l4mC ![]() 1l5oC ![]() 1d0sS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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Unit cell |
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Details | The biological assembly is a dimer generated from one monomer in asymmetric unit by crystallographic two-fold axis |
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Components
#1: Protein | Mass: 36675.594 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() References: UniProt: Q05603, nicotinate-nucleotide-dimethylbenzimidazole phosphoribosyltransferase |
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#2: Chemical | ChemComp-RBZ / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.1 Å3/Da / Density % sol: 41.39 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6 Details: ammonium phosphate at pH 6.0, VAPOR DIFFUSION, HANGING DROP at 298K |
-Data collection
Diffraction | Mean temperature: 278 K |
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Diffraction source | Source: ![]() |
Detector | Type: SIEMENS HI-STAR / Detector: AREA DETECTOR / Details: double focusing mirror |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Highest resolution: 2 Å / Num. all: 20503 / Num. obs: 20503 / % possible obs: 88.9 % / Redundancy: 3.1 % / Rmerge(I) obs: 0.049 / Net I/σ(I): 13.2 |
Reflection shell | Resolution: 2→2.06 Å / Redundancy: 1.9 % / Rmerge(I) obs: 0.157 / Mean I/σ(I) obs: 2.9 / % possible all: 68.1 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB entry 1D0S Resolution: 2→500 Å / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
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Refinement step | Cycle: LAST / Resolution: 2→500 Å
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Refine LS restraints |
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