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Yorodumi- PDB-1dnl: X-RAY STRUCTURE OF ESCHERICHIA COLI PYRIDOXINE 5'-PHOSPHATE OXIDA... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1dnl | ||||||
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Title | X-RAY STRUCTURE OF ESCHERICHIA COLI PYRIDOXINE 5'-PHOSPHATE OXIDASE COMPLEXED WITH FMN AT 1.8 ANGSTROM RESOLUTION | ||||||
Components | PYRIDOXINE 5'-PHOSPHATE OXIDASE | ||||||
Keywords | OXIDOREDUCTASE / BETA BARREL / PROTEIN-FMN COMPLEX | ||||||
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 K12 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.8 Å | ||||||
Authors | Safo, M.K. / Mathews, I. / Musayev, F.N. / di Salvo, M.L. / Thiel, D.J. / Abraham, D.J. / Schirch, V. | ||||||
Citation | Journal: Structure Fold.Des. / Year: 2000 Title: X-ray structure of Escherichia coli pyridoxine 5'-phosphate oxidase complexed with FMN at 1.8 A resolution. Authors: Safo, M.K. / Mathews, I. / Musayev, F.N. / di Salvo, M.L. / Thiel, D.J. / Abraham, D.J. / Schirch, V. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1dnl.cif.gz | 54.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1dnl.ent.gz | 42.5 KB | Display | PDB format |
PDBx/mmJSON format | 1dnl.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1dnl_validation.pdf.gz | 779.4 KB | Display | wwPDB validaton report |
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Full document | 1dnl_full_validation.pdf.gz | 786.7 KB | Display | |
Data in XML | 1dnl_validation.xml.gz | 12.4 KB | Display | |
Data in CIF | 1dnl_validation.cif.gz | 16.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dn/1dnl ftp://data.pdbj.org/pub/pdb/validation_reports/dn/1dnl | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 23439.182 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli K12 (bacteria) / Species: Escherichia coli / Strain: K-12 / Plasmid: PET22B / Production host: Escherichia coli (E. coli) References: UniProt: P28225, UniProt: P0AFI7*PLUS, pyridoxal 5'-phosphate synthase |
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#2: Chemical | ChemComp-PO4 / |
#3: Chemical | ChemComp-FMN / |
#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: 2.77 Å3/Da / Density % sol: 55.2 % | ||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7 Details: AMMONIUM FORMATE, HEPES OR MES, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K | ||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 22 ℃ / pH: 7.5 | ||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.82944 |
Detector | Type: APS / Detector: CCD / Date: Jan 1, 1999 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.82944 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→55 Å / Num. all: 26980 / Num. obs: 26980 / % possible obs: 96.3 % / Observed criterion σ(I): 0 / Redundancy: 9.7 % / Biso Wilson estimate: 16.1 Å2 / Rmerge(I) obs: 0.075 / Net I/σ(I): 7.6 |
Reflection shell | Resolution: 1.8→1.86 Å / Redundancy: 5 % / Rmerge(I) obs: 0.357 / % possible all: 74.2 |
Reflection | *PLUS Num. measured all: 262844 |
Reflection shell | *PLUS % possible obs: 74.2 % |
-Processing
Software |
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Refinement | Resolution: 1.8→55 Å / Rfactor Rfree error: 0.006 / Data cutoff high rms absF: 1573005.61 / Isotropic thermal model: restrained / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: ENGH & HUBER / Details: USED BULK SOLVENT CORRECTION
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Solvent computation | Solvent model: flat model / Bsol: 43.517 Å2 / ksol: 0.362461 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 25.4 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.8→55 Å
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Refine LS restraints |
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Refine LS restraints NCS | NCS model details: none | ||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 1.8→1.91 Å / Rfactor Rfree error: 0.02 / Total num. of bins used: 6
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Software | *PLUS Name: CNS / Classification: refinement | ||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor Rwork: 0.233 |