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Yorodumi- PDB-1g79: X-RAY STRUCTURE OF ESCHERICHIA COLI PYRIDOXINE 5'-PHOSPHATE OXIDA... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1g79 | ||||||
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Title | X-RAY STRUCTURE OF ESCHERICHIA COLI PYRIDOXINE 5'-PHOSPHATE OXIDASE COMPLEXED WITH PYRIDOXAL 5'-PHOSPHATE AT 2.0 A RESOLUTION | ||||||
Components | PYRIDOXINE 5'-PHOSPHATE OXIDASEPyridoxine 5′-phosphate oxidase | ||||||
Keywords | OXIDOREDUCTASE / PLP complex / FMN complex / pyridoxine 5'-phosphate | ||||||
Function / homology | Function and homology information 'de novo' pyridoxal 5'-phosphate biosynthetic process / pyridoxal 5'-phosphate synthase / pyridoxamine phosphate oxidase activity / riboflavin binding / pyridoxal phosphate biosynthetic process / pyridoxine biosynthetic process / phosphate ion binding / pyridoxal phosphate binding / FMN binding / oxidoreductase activity ...'de novo' pyridoxal 5'-phosphate biosynthetic process / pyridoxal 5'-phosphate synthase / pyridoxamine phosphate oxidase activity / riboflavin binding / pyridoxal phosphate biosynthetic process / pyridoxine biosynthetic process / phosphate ion binding / pyridoxal phosphate binding / FMN binding / oxidoreductase activity / protein homodimerization activity / protein-containing complex / cytosol Similarity search - Function | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / FOURIER SYNTHESIS / Resolution: 2 Å | ||||||
Authors | Safo, M.K. / Musayev, F.N. / di Salvo, M.L. / Schirch, V. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2001 Title: X-ray structure of Escherichia coli pyridoxine 5'-phosphate oxidase complexed with pyridoxal 5'-phosphate at 2.0 A resolution. Authors: Safo, M.K. / Musayev, F.N. / di Salvo, M.L. / Schirch, V. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1g79.cif.gz | 61.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1g79.ent.gz | 43.9 KB | Display | PDB format |
PDBx/mmJSON format | 1g79.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/g7/1g79 ftp://data.pdbj.org/pub/pdb/validation_reports/g7/1g79 | HTTPS FTP |
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-Related structure data
Related structure data | 1g76C 1g77C 1g78C 1dnlS C: citing same article (ref.) S: Starting model for refinement |
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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 constructued from chain A symmetry partner generated by the two-fold axis |
-Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 25585.188 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Plasmid: PET22B / Production host: Escherichia coli (E. coli) References: UniProt: P28225, UniProt: P0AFI7*PLUS, pyridoxal 5'-phosphate synthase |
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-Non-polymers , 5 types, 150 molecules
#2: Chemical | #3: Chemical | ChemComp-FMN / | #4: Chemical | #5: Chemical | ChemComp-BME / | #6: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.85 Å3/Da / Density % sol: 56.8 % | ||||||||||||||||||||
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7 Details: Ammonium sulfate and MES, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K | ||||||||||||||||||||
Crystal grow | *PLUS pH: 6.2 / Details: macroseeding | ||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 98 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å |
Detector | Type: RIGAKU RAXIS II / Detector: IMAGE PLATE / Date: Mar 24, 2000 / Details: mirrors |
Radiation | Monochromator: MSC mirrors / Protocol: LAUE / Monochromatic (M) / Laue (L): L / Scattering type: neutron |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2→55 Å / Num. all: 20202 / Num. obs: 20202 / % possible obs: 98.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.5 % / Biso Wilson estimate: 19.8 Å2 / Rmerge(I) obs: 0.056 / Rsym value: 0.051 / Net I/σ(I): 12.3 |
Reflection shell | Resolution: 2→2.1 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.251 / Mean I/σ(I) obs: 3.3 / Num. unique all: 2659 / % possible all: 97.7 |
Reflection | *PLUS Num. measured all: 71938 |
Reflection shell | *PLUS % possible obs: 97.7 % / Num. possible: 8521 / Num. unique obs: 2659 |
-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS Starting model: PDB entry 1DNL Resolution: 2→55 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 78166.34 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh and Huber / Details: bulk solvent correction
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 44.73 Å2 / ksol: 0.356 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 32.1 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2→55 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2→2.13 Å / Rfactor Rfree error: 0.019 / Total num. of bins used: 6
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Xplor file |
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Software | *PLUS Name: CNS / Version: 0.5 / Classification: refinement | ||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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