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- PDB-2og7: Cystal structure of asparagine oxygenase in complex with Fe(II), ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 2og7 | ||||||
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Title | Cystal structure of asparagine oxygenase in complex with Fe(II), 2S,3S-3-hydroxyasparagine and succinate | ||||||
![]() | asparagine oxygenase | ||||||
![]() | OXIDOREDUCTASE / ELECTRON TRANSPORT / nonribosomal peptide synthesis / non-heme iron(II) / alpha-ketoglutarate oxygenase / beta-hydroxylated amino acid | ||||||
Function / homology | ![]() L-asparagine hydroxylase / antibiotic biosynthetic process / oxidoreductase activity / iron ion binding Similarity search - Function | ||||||
Biological species | Streptomyces coelicolor A3 | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Essen, L.-O. / Strieker, M. | ||||||
![]() | ![]() Title: Mechanistic and structural basis of stereospecific Cbeta-hydroxylation in calcium-dependent antibiotic, a daptomycin-type lipopeptide Authors: Strieker, M. / Kopp, F. / Mahlert, C. / Essen, L.-O. / Marahiel, M.A. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 84.5 KB | Display | ![]() |
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PDB format | ![]() | 60.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 456.2 KB | Display | ![]() |
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Full document | ![]() | 458.9 KB | Display | |
Data in XML | ![]() | 16.4 KB | Display | |
Data in CIF | ![]() | 24.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2og5C ![]() 2og6C ![]() 1dryS C: citing same article ( S: Starting model for refinement |
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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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Components on special symmetry positions |
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Components
#1: Protein | Mass: 38949.574 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Species: Streptomyces coelicolor / Strain: DSMZ 40783 Description: expression plasmid encodes for N-terminal His-7-tag for IMAC Gene: sco3236 (asnO) / Plasmid: pQTEVMS01 / Species (production host): Escherichia coli / Production host: ![]() ![]() |
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#2: Chemical | ChemComp-FE2 / |
#3: Chemical | ChemComp-SIN / |
#4: Chemical | ChemComp-AHB / |
#5: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.81 Å3/Da / Density % sol: 56.15 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 4.6 Details: 2.5 M sodium acetate, 0.1 M Hepes, pH 4.6, VAPOR DIFFUSION, SITTING DROP, temperature 291K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MAR CCD 165 mm / Detector: CCD / Date: Jun 30, 2006 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.808 Å / Relative weight: 1 |
Reflection | Resolution: 1.65→23 Å / Num. obs: 51815 / % possible obs: 99.4 % / Observed criterion σ(F): 191425 / Redundancy: 3.69 % / Biso Wilson estimate: 24.9 Å2 / Rmerge(I) obs: 0.052 / Net I/σ(I): 15.1 |
Reflection shell | Resolution: 1.65→1.74 Å / Redundancy: 3.49 % / Rmerge(I) obs: 0.539 / Mean I/σ(I) obs: 1.7 / Num. unique all: 7385 / % possible all: 98.4 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB Entry 1DRY Resolution: 1.66→22.91 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.963 / SU B: 3.518 / SU ML: 0.053 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.074 / ESU R Free: 0.072 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 23.14 Å2
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Refinement step | Cycle: LAST / Resolution: 1.66→22.91 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.66→1.702 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Origin x: -5.2883 Å / Origin y: 62.4197 Å / Origin z: -12.455 Å
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Refinement TLS group | Selection: ALL |