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Yorodumi- PDB-2wbp: Crystal structure of VioC in complex with Fe(II), (2S,3S)- hydrox... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2wbp | |||||||||
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Title | Crystal structure of VioC in complex with Fe(II), (2S,3S)- hydroxyarginine, and succinate | |||||||||
Components | L-ARGININE BETA-HYDROXYLASE | |||||||||
Keywords | OXIDOREDUCTASE / NON-HEME FE(II) HYDROXYLASE / CBETA-HYDROXYLATION / NRPS / VIOMYCIN / ALPHA-KETOGLUTARATE | |||||||||
Function / homology | Function and homology information L-arginine hydroxylase / 2-oxoglutarate, L-arginine oxygenase (succinate-forming) activity / 2-oxoglutarate-dependent dioxygenase activity / antibiotic biosynthetic process / iron ion binding / membrane Similarity search - Function | |||||||||
Biological species | STREPTOMYCES VINACEUS (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.16 Å | |||||||||
Authors | Helmetag, V. / Samel, S.A. / Thomas, M.G. / Marahiel, M.A. / Essen, L.-O. | |||||||||
Citation | Journal: FEBS J. / Year: 2009 Title: Structural Basis for the Erythro-Stereospecificity of the L-Arginine Oxygenase Vioc in Viomycin Biosynthesis. Authors: Helmetag, V. / Samel, S.A. / Thomas, M.G. / Marahiel, M.A. / Essen, L.-O. | |||||||||
History |
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Remark 700 | SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2wbp.cif.gz | 170 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2wbp.ent.gz | 132.9 KB | Display | PDB format |
PDBx/mmJSON format | 2wbp.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wb/2wbp ftp://data.pdbj.org/pub/pdb/validation_reports/wb/2wbp | HTTPS FTP |
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-Related structure data
Related structure data | 2wboC 2wbqC 2og5S 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
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 39481.199 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) STREPTOMYCES VINACEUS (bacteria) / Plasmid: PET28VIOC / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q6WZB0 |
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-Non-polymers , 6 types, 392 molecules
#2: Chemical | ChemComp-ARG / |
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#3: Chemical | ChemComp-FE2 / |
#4: Chemical | ChemComp-ZZU / ( |
#5: Chemical | ChemComp-SIN / |
#6: Chemical | ChemComp-GOL / |
#7: 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: 2.03 Å3/Da / Density % sol: 39.53 % / Description: NONE |
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Crystal grow | pH: 8.5 Details: 1.0 M NA-SUCCINATE, 0.1 M TRIS/HCL PH 8.0, 3 MM (2S\,3S)-HYDROXYARGININE |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.8726 |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Jul 4, 2008 / Details: MIRRORS |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.8726 Å / Relative weight: 1 |
Reflection | Resolution: 1.16→20 Å / Num. obs: 99570 / % possible obs: 91.3 % / Observed criterion σ(I): -3 / Redundancy: 3 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 10.6 |
Reflection shell | Resolution: 1.16→1.19 Å / Rmerge(I) obs: 0.25 / Mean I/σ(I) obs: 2.1 / % possible all: 51.1 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2OG5 Resolution: 1.16→19.96 Å / Cor.coef. Fo:Fc: 0.98 / Cor.coef. Fo:Fc free: 0.968 / SU B: 1.216 / SU ML: 0.025 / Cross valid method: THROUGHOUT / ESU R: 0.034 / ESU R Free: 0.037 / 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: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 13.984 Å2
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Refinement step | Cycle: LAST / Resolution: 1.16→19.96 Å
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