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Yorodumi- PDB-4ne0: Crystal structure of non-heme iron oxygenase OrfP D157A mutant in... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4ne0 | |||||||||
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Title | Crystal structure of non-heme iron oxygenase OrfP D157A mutant in complex with (3S)-hydroxy-L-Arg | |||||||||
Components | L-arginine beta-hydroxylase | |||||||||
Keywords | HYDROLASE / oxygenase / hydroxylase | |||||||||
Function / homology | Function and homology information L-arginine hydroxylase / 2-oxoglutarate, L-arginine oxygenase (succinate-forming) activity / iron ion binding Similarity search - Function | |||||||||
Biological species | Streptomyces lavendulae (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.17 Å | |||||||||
Authors | Chang, C.Y. / Liu, Y.C. / Lyu, S.Y. / Wu, C.C. / Li, T.L. | |||||||||
Citation | Journal: Angew.Chem.Int.Ed.Engl. / Year: 2014 Title: Biosynthesis of streptolidine involved two unexpected intermediates produced by a dihydroxylase and a cyclase through unusual mechanisms Authors: Chang, C.Y. / Lyu, S.Y. / Liu, Y.C. / Hsu, N.S. / Wu, C.C. / Tang, C.F. / Lin, K.H. / Ho, J.Y. / Wu, C.J. / Tsai, M.D. / Li, T.L. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4ne0.cif.gz | 274 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4ne0.ent.gz | 219.5 KB | Display | PDB format |
PDBx/mmJSON format | 4ne0.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ne/4ne0 ftp://data.pdbj.org/pub/pdb/validation_reports/ne/4ne0 | HTTPS FTP |
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-Related structure data
Related structure data | 4m23SC 4m25C 4m26C 4m27C 4m2cC 4m2eC 4m2fC 4m2gC 4m2iC 4m2jC 4m2kC 4m2mC S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 41144.074 Da / Num. of mol.: 4 / Mutation: D157A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Streptomyces lavendulae (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: G9MBV2 #2: Chemical | ChemComp-FE / #3: Chemical | #4: Chemical | #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.32 Å3/Da / Density % sol: 46.92 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 20% PEG 3350, 0.2M NaF, 0.1M Bis-Tris propane, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 80 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSRRC / Beamline: BL15A / Wavelength: 1 Å |
Detector | Type: RAYONIX MX300HE / Detector: CCD / Date: Oct 26, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.17→30 Å / Num. all: 76451 / Num. obs: 76451 / % possible obs: 97.2 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 |
Reflection shell | Resolution: 2.18→2.26 Å / % possible all: 99.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4M23 Resolution: 2.17→30 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.912 / SU B: 6.754 / SU ML: 0.172 / Cross valid method: THROUGHOUT / ESU R: 0.281 / ESU R Free: 0.23 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 41.889 Å2
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Refinement step | Cycle: LAST / Resolution: 2.17→30 Å
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Refine LS restraints |
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