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Yorodumi- PDB-2wbq: Crystal structure of VioC in complex with (2S,3S)-hydroxyarginine -
+Open data
-Basic information
Entry | Database: PDB / ID: 2wbq | |||||||||
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Title | Crystal structure of VioC in complex with (2S,3S)-hydroxyarginine | |||||||||
Components | L-ARGININE BETA-HYDROXYLASE | |||||||||
Keywords | OXIDOREDUCTASE / NON-HEME FE(II) HYDROXYLASE / CBETA-HYDROXYLATION / L-ARGININE OXYGENASE / 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: 1.1 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 | 2wbq.cif.gz | 170.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2wbq.ent.gz | 134.7 KB | Display | PDB format |
PDBx/mmJSON format | 2wbq.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2wbq_validation.pdf.gz | 453.5 KB | Display | wwPDB validaton report |
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Full document | 2wbq_full_validation.pdf.gz | 461.8 KB | Display | |
Data in XML | 2wbq_validation.xml.gz | 20.3 KB | Display | |
Data in CIF | 2wbq_validation.cif.gz | 31.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wb/2wbq ftp://data.pdbj.org/pub/pdb/validation_reports/wb/2wbq | HTTPS FTP |
-Related structure data
Related structure data | 2wboC 2wbpC 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 on special symmetry positions |
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-Components
#1: Protein | Mass: 39453.184 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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#2: Chemical | ChemComp-ACT / |
#3: Chemical | ChemComp-ZZU / ( |
#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: 2.03 Å3/Da / Density % sol: 39.38 % / Description: NONE |
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Crystal grow | pH: 7.5 Details: 0.6 M TRI-SODIUM CITRATE 0.1 M HEPES PH 7.5 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: 1.1→20 Å / Num. obs: 123576 / % possible obs: 96.8 % / Observed criterion σ(I): -3 / Redundancy: 3.6 % / Rmerge(I) obs: 0.04 / Net I/σ(I): 14.1 |
Reflection shell | Resolution: 1.1→1.13 Å / Rmerge(I) obs: 0.57 / Mean I/σ(I) obs: 1.5 / % possible all: 84.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2OG5 Resolution: 1.1→19.75 Å / Cor.coef. Fo:Fc: 0.982 / Cor.coef. Fo:Fc free: 0.97 / SU B: 1.336 / SU ML: 0.027 / Cross valid method: THROUGHOUT / ESU R: 0.03 / ESU R Free: 0.032 / 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: 14.18 Å2
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Refinement step | Cycle: LAST / Resolution: 1.1→19.75 Å
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