[English] 日本語
Yorodumi- PDB-1jhq: Three-dimensional Structure of CobT in Complex with Reaction Prod... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1jhq | ||||||
---|---|---|---|---|---|---|---|
Title | Three-dimensional Structure of CobT in Complex with Reaction Products of 5-methoxybenzimidazole and NaMN | ||||||
Components | Nicotinate Mononucleotide:5,6-Dimethylbenzimidazole Phosphoribosyltransferase | ||||||
Keywords | TRANSFERASE / CobT / Cobalamin Biosynthesis / Lower ligand / Cobamides / NN:DBI PRT / N1-Alpha-Phosphoribosyltransferase | ||||||
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: J.Biol.Chem. / Year: 2001 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. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 1jhq.cif.gz | 78.7 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb1jhq.ent.gz | 57.3 KB | Display | PDB format |
PDBx/mmJSON format | 1jhq.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1jhq_validation.pdf.gz | 732 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 1jhq_full_validation.pdf.gz | 740.7 KB | Display | |
Data in XML | 1jhq_validation.xml.gz | 16.5 KB | Display | |
Data in CIF | 1jhq_validation.cif.gz | 23.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/jh/1jhq ftp://data.pdbj.org/pub/pdb/validation_reports/jh/1jhq | HTTPS FTP |
-Related structure data
Related structure data | 1jh8C 1jhaC 1jhmC 1jhoC 1jhpC 1jhrC 1jhuC 1jhvC 1jhxC 1jhyC 1d0sS S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-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) / Production host: Salmonella enterica (bacteria) References: UniProt: Q05603, nicotinate-nucleotide-dimethylbenzimidazole phosphoribosyltransferase |
---|---|
#2: Chemical | ChemComp-PMO / |
#3: Chemical | ChemComp-NIO / |
#4: Water | ChemComp-HOH / |
Has protein modification | Y |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.1 Å3/Da / Density % sol: 41.35 % | ||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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
|
-Data collection
Diffraction | Mean temperature: 278 K |
---|---|
Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.54184 |
Detector | Type: SIEMENS HI-STAR / Detector: AREA DETECTOR / Date: Aug 25, 2000 / Details: Mirrors |
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: 20523 / % possible obs: 88.9 % / Redundancy: 3.2 % / Rmerge(I) obs: 0.046 / Net I/σ(I): 12.8 |
Reflection shell | Resolution: 2→2.06 Å / Redundancy: 1.6 % / Rmerge(I) obs: 0.115 / Mean I/σ(I) obs: 3.7 / % possible all: 67.8 |
Reflection shell | *PLUS % possible obs: 67.8 % |
-Processing
Software |
| ||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: FOURIER SYNTHESIS Starting model: 1D0S Resolution: 2→30 Å / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
| ||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2→30 Å
| ||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||
Software | *PLUS Name: TNT / Classification: refinement | ||||||||||||||||||||
Refinement | *PLUS Highest resolution: 2 Å / Lowest resolution: 30 Å / σ(F): 0 / % reflection Rfree: 10 % / Rfactor obs: 0.178 | ||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||
Refine LS restraints | *PLUS
|