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Open data
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Basic information
Entry | Database: PDB / ID: 4m23 | ||||||
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Title | Crystal structure of non-heme iron oxygenase OrfP | ||||||
![]() | L-arginine beta-hydroxylase | ||||||
![]() | OXIDOREDUCTASE / hydroxylase / Fe binding | ||||||
Function / homology | ![]() L-arginine hydroxylase / 2-oxoglutarate, L-arginine oxygenase (succinate-forming) activity / iron ion binding Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Chang, C.Y. / Liu, Y.C. / Lyu, S.Y. / Wu, C.C. / Li, T.L. | ||||||
![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 289.5 KB | Display | ![]() |
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PDB format | ![]() | 233.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 460.7 KB | Display | ![]() |
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Full document | ![]() | 485.8 KB | Display | |
Data in XML | ![]() | 57.7 KB | Display | |
Data in CIF | ![]() | 86.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4m25C ![]() 4m26C ![]() 4m27C ![]() 4m2cC ![]() 4m2eC ![]() 4m2fC ![]() 4m2gC ![]() 4m2iC ![]() 4m2jC ![]() 4m2kC ![]() 4m2mC ![]() 4ne0C ![]() 2wboS 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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2 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 41188.082 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.35 Å3/Da / Density % sol: 47.55 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion / pH: 7.5 Details: 100mM Bis Tris Propane, 200mM NaF, 20% PEG 3350, pH 7.5, VAPOR DIFFUSION, temperature 293K |
-Data collection
Diffraction | Mean temperature: 80 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 14, 2013 |
Radiation | Monochromator: Horizontally Focusing Single Crystal Monochromator Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9762 Å / Relative weight: 1 |
Reflection | Resolution: 1.76→30 Å / Num. all: 150128 / Num. obs: 142562 / % possible obs: 99.9 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 |
Reflection shell | Resolution: 1.76→1.82 Å / % possible all: 99.9 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 2WBO Resolution: 1.76→30 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.942 / SU B: 2.554 / SU ML: 0.082 / Cross valid method: THROUGHOUT / ESU R: 0.118 / ESU R Free: 0.115 / 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: 30.293 Å2
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Refinement step | Cycle: LAST / Resolution: 1.76→30 Å
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Refine LS restraints |
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