+Open data
-Basic information
Entry | Database: PDB / ID: 2og6 | ||||||
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Title | Crystal structure of asparagine oxygenase in complex with Fe(II) | ||||||
Components | asparagine oxygenase | ||||||
Keywords | OXIDOREDUCTASE / ELECTRON TRANSPORT / nonribosomal peptide synthesis / non-heme iron(II) / alpha-ketoglutarate oxygenase / beta-hydroxylated amino acid | ||||||
Function / homology | Function and homology information L-asparagine hydroxylase / antibiotic biosynthetic process / oxidoreductase activity / iron ion binding Similarity search - Function | ||||||
Biological species | Streptomyces coelicolor A3 | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.916 Å | ||||||
Authors | Essen, L.-O. / Strieker, M. | ||||||
Citation | Journal: Acs Chem.Biol. / Year: 2007 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2og6.cif.gz | 84.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2og6.ent.gz | 60.7 KB | Display | PDB format |
PDBx/mmJSON format | 2og6.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2og6_validation.pdf.gz | 434 KB | Display | wwPDB validaton report |
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Full document | 2og6_full_validation.pdf.gz | 437.7 KB | Display | |
Data in XML | 2og6_validation.xml.gz | 16.1 KB | Display | |
Data in CIF | 2og6_validation.cif.gz | 23.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/og/2og6 ftp://data.pdbj.org/pub/pdb/validation_reports/og/2og6 | HTTPS FTP |
-Related structure data
Related structure data | 2og5C 2og7C 1dryS 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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-Components
#1: Protein | Mass: 38949.574 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Streptomyces coelicolor A3(2) (bacteria) 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: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q9Z4Z5 | ||
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#2: Chemical | ChemComp-FE2 / | ||
#3: Chemical | #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: 2.74 Å3/Da / Density % sol: 55.06 % |
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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: ROTATING ANODE / Type: OTHER / Wavelength: 1.5418 Å |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→20 Å / Num. obs: 33610 / % possible obs: 98.6 % / Observed criterion σ(F): 260083 / Redundancy: 7.74 % / Biso Wilson estimate: 30.6 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 38.3 |
Reflection shell | Resolution: 1.9→1.93 Å / Rmerge(I) obs: 0.416 / Mean I/σ(I) obs: 2.1 / Num. unique all: 1331 / % possible all: 78.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1DRY Resolution: 1.916→20 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.953 / SU B: 5.701 / SU ML: 0.076 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.118 / ESU R Free: 0.111 / 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: 34.046 Å2
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Refinement step | Cycle: LAST / Resolution: 1.916→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.916→1.966 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Origin x: -5.3549 Å / Origin y: 62.2181 Å / Origin z: -12.8026 Å
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Refinement TLS group | Selection: ALL |