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- PDB-1jha: Structural Investigation of the Biosynthesis of Alternative Lower... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1jha | ||||||
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Title | Structural Investigation of the Biosynthesis of Alternative Lower Ligands for Cobamides by Nicotinate Mononucleotide:5,6-Dimethylbenzimidazole Phosphoribosyltransferase (CobT) from Salmonella enterica | ||||||
![]() | Nicotinate Mononucleotide:5,6-Dimethylbenzimidazole Phosphoribosyltransferase | ||||||
![]() | TRANSFERASE / CobT / Cobalamin Biosynthesis / NN:DBI PRT / N1-Alpha-Phosphoribosyltransferase | ||||||
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: Structural investigation of the biosynthesis of alternative lower ligands for cobamides by nicotinate mononucleotide: 5,6-dimethylbenzimidazole phosphoribosyltransferase from Salmonella enterica. Authors: Cheong, C.G. / Escalante-Semerena, J.C. / Rayment, I. | ||||||
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 78.6 KB | Display | ![]() |
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PDB format | ![]() | 56.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 769.2 KB | Display | ![]() |
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Full document | ![]() | 776.9 KB | Display | |
Data in XML | ![]() | 16.3 KB | Display | |
Data in CIF | ![]() | 23.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1jh8C ![]() 1jhmC ![]() 1jhoC ![]() 1jhpC ![]() 1jhqC ![]() 1jhrC ![]() 1jhuC ![]() 1jhvC ![]() 1jhxC ![]() 1jhyC ![]() 1dosS C: citing same article ( S: Starting model for refinement |
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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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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-AAM / |
#3: Chemical | ChemComp-NIO / |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.09 Å3/Da / Density % sol: 41.15 % | ||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6 Details: Ammonium Phosphate, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K | ||||||||||||||||||||||||||||||
Crystal grow | *PLUS pH: 7.5 | ||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 278 K |
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Diffraction source | Source: ![]() |
Detector | Type: SIEMENS HI-STAR / Detector: AREA DETECTOR / Date: Nov 10, 2000 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54184 Å / Relative weight: 1 |
Reflection | Resolution: 2→30 Å / Num. obs: 20370 / Redundancy: 3.1 % / Rmerge(I) obs: 0.051 / Net I/σ(I): 11.4 |
Reflection shell | Resolution: 2→2.06 Å / Redundancy: 1.5 % / Rmerge(I) obs: 0.132 / Mean I/σ(I) obs: 3.3 |
Reflection | *PLUS Lowest resolution: 30 Å / % possible obs: 89 % |
Reflection shell | *PLUS % possible obs: 68.8 % |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1DOS Resolution: 2→30 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Refinement step | Cycle: LAST / Resolution: 2→30 Å
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Refine LS restraints |
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Software | *PLUS Name: TNT / Classification: refinement | ||||||||||||||||||||
Refinement | *PLUS Highest resolution: 2 Å / σ(F): 0 / % reflection Rfree: 10 % / Rfactor obs: 0.178 | ||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||
Refine LS restraints | *PLUS
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