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Yorodumi- PDB-1l5m: Crystal Structure of CobT complexed with N7-(5'-phosphoribosyl)-2... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1l5m | ||||||
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Title | Crystal Structure of CobT complexed with N7-(5'-phosphoribosyl)-2-aminopurine and nicotinate | ||||||
Components | Nicotinate-nucleotide--dimethylbenzimidazole phosphoribosyltransferase | ||||||
Keywords | TRANSFERASE / CobT / cobalamin synthetic enzyme / phosphoribosyltransferase / 5 / 6-dimethylbenzimidazole / nicotinate mononucleotide | ||||||
Function / homology | Function and homology information nicotinate-nucleotide-dimethylbenzimidazole phosphoribosyltransferase / nicotinate-nucleotide-dimethylbenzimidazole phosphoribosyltransferase activity / cobalamin biosynthetic process / nucleotide binding Similarity search - Function | ||||||
Biological species | Salmonella enterica (bacteria) | ||||||
Method | X-RAY DIFFRACTION / FOURIER SYNTHESIS / Resolution: 2 Å | ||||||
Authors | Cheong, C.-G. / Escalante-Semerena, J. / Rayment, I. | ||||||
Citation | Journal: Biochemistry / Year: 2002 Title: Structural studies of the L-threonine-O-3-phosphate decarboxylase (CobD) enzyme from Salmonella enterica: the apo, substrate, and product-aldimine complexes. Authors: Cheong, C.G. / Escalante-Semerena, J.C. / Rayment, I. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1l5m.cif.gz | 77.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1l5m.ent.gz | 56.1 KB | Display | PDB format |
PDBx/mmJSON format | 1l5m.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1l5m_validation.pdf.gz | 776.7 KB | Display | wwPDB validaton report |
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Full document | 1l5m_full_validation.pdf.gz | 781.5 KB | Display | |
Data in XML | 1l5m_validation.xml.gz | 15.8 KB | Display | |
Data in CIF | 1l5m_validation.cif.gz | 22.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/l5/1l5m ftp://data.pdbj.org/pub/pdb/validation_reports/l5/1l5m | HTTPS FTP |
-Related structure data
Related structure data | 1l4nC 1l5fC 1l5kC 1l5lC 1l5nC 1lc5C 1lc7C 1lc8C 1d0sS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-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 |
-Components
#1: Protein | Mass: 36675.594 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Salmonella enterica (bacteria) / Gene: cobt / Plasmid: pT7-5 / Production host: Salmonella enterica (bacteria) / Strain (production host): JE2461 References: UniProt: Q05603, nicotinate-nucleotide-dimethylbenzimidazole phosphoribosyltransferase |
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#2: Chemical | ChemComp-7RA / |
#3: Chemical | ChemComp-NIO / |
#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: 2.1 Å3/Da / Density % sol: 41.52 % |
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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 at 298K |
-Data collection
Diffraction | Mean temperature: 298 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å |
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: 19462 / Num. obs: 19462 / % possible obs: 88.7 % / Redundancy: 3.1 % / Rmerge(I) obs: 0.063 / Net I/σ(I): 8.7 |
Reflection shell | Resolution: 2→2.06 Å / Redundancy: 1.6 % / Rmerge(I) obs: 0.173 / Mean I/σ(I) obs: 2.6 / % possible all: 66.8 |
-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS 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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