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- PDB-1g76: X-RAY STRUCTURE OF ESCHERICHIA COLI PYRIDOXINE 5'-PHOSPHATE OXIDA... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1g76 | ||||||
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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 | ||||||
![]() | PYRIDOXINE 5`-PHOSPHATE OXIDASE | ||||||
![]() | OXIDOREDUCTASE / PLP complex / FMN complex / pyridoxine 5'-phosphate | ||||||
Function / homology | ![]() '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 | ![]() ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Safo, M.K. / Musayev, F.N. / di Salvo, M.L. / Schirch, V. | ||||||
![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 58.3 KB | Display | ![]() |
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PDB format | ![]() | 41.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 787.6 KB | Display | ![]() |
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Full document | ![]() | 797.8 KB | Display | |
Data in XML | ![]() | 12.2 KB | Display | |
Data in CIF | ![]() | 15.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1g77C ![]() 1g78C ![]() 1g79C ![]() 1dnlS 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, which was constructued from chain A and its symmetry partner generated by the two-fold axis |
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Components
#1: Protein | Mass: 25585.188 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() References: UniProt: P28225, UniProt: P0AFI7*PLUS, pyridoxal 5'-phosphate synthase | ||||||
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#2: Chemical | #3: Chemical | ChemComp-FMN / | #4: Chemical | ChemComp-PLP / | #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.82 Å3/Da / Density % sol: 56.35 % | ||||||||||||||||||||
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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: ![]() |
Detector | Type: RIGAKU RAXIS II / Detector: IMAGE PLATE / Date: Mar 29, 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: 2.2→55 Å / Num. all: 14882 / Num. obs: 14882 / % possible obs: 95.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.9 % / Biso Wilson estimate: 25.6 Å2 / Rmerge(I) obs: 0.055 / Rsym value: 5.8 / Net I/σ(I): 12.1 |
Reflection shell | Resolution: 2.2→2.3 Å / Redundancy: 2.6 % / Rmerge(I) obs: 0.232 / Mean I/σ(I) obs: 2.2 / Num. unique all: 1772 / % possible all: 94.1 |
Reflection | *PLUS Num. measured all: 43602 |
Reflection shell | *PLUS % possible obs: 94.1 % / Num. possible: 4588 / Num. unique obs: 1772 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB entry 1DNL Resolution: 2.2→55 Å / Rfactor Rfree error: 0.01 / Data cutoff high absF: 87008.93 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 1 / Stereochemistry target values: Engh and Huber / Details: bulk solvent correction
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 58.57 Å2 / ksol: 0.38 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 45.4 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.2→55 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.2→2.34 Å / Rfactor Rfree error: 0.034 / 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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