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- PDB-6x0i: Structure of oxidized SidA ornithine hydroxylase with the FAD "in... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6x0i | |||||||||
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Title | Structure of oxidized SidA ornithine hydroxylase with the FAD "in" and complexed with NADP | |||||||||
![]() | L-ornithine N(5)-monooxygenase | |||||||||
![]() | OXIDOREDUCTASE / FLAVIN-CONTAINING MONOOXYGENASE / FLAVOPROTEIN | |||||||||
Function / homology | ![]() L-ornithine N5-monooxygenase [NAD(P)H] / ferrichrome biosynthetic process / ornithine N5-monooxygenase activity / siderophore-dependent iron import into cell / cellular response to iron ion starvation / siderophore biosynthetic process / N,N-dimethylaniline monooxygenase activity / ergosterol biosynthetic process / NADP+ binding / secondary metabolite biosynthetic process ...L-ornithine N5-monooxygenase [NAD(P)H] / ferrichrome biosynthetic process / ornithine N5-monooxygenase activity / siderophore-dependent iron import into cell / cellular response to iron ion starvation / siderophore biosynthetic process / N,N-dimethylaniline monooxygenase activity / ergosterol biosynthetic process / NADP+ binding / secondary metabolite biosynthetic process / monooxygenase activity / intracellular iron ion homeostasis / iron ion binding Similarity search - Function | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Tanner, J.J. / Campbell, A.C. | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Trapping conformational states of a flavin-dependent N -monooxygenase in crystallo reveals protein and flavin dynamics. Authors: Campbell, A.C. / Stiers, K.M. / Martin Del Campo, J.S. / Mehra-Chaudhary, R. / Sobrado, P. / Tanner, J.J. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 736.5 KB | Display | ![]() |
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PDB format | ![]() | 605.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 2.8 MB | Display | ![]() |
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Full document | ![]() | 2.8 MB | Display | |
Data in XML | ![]() | 74.7 KB | Display | |
Data in CIF | ![]() | 105.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6x0hC ![]() 6x0jC ![]() 6x0kC ![]() 4b63S S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
-Protein , 1 types, 4 molecules ABCD
#1: Protein | Mass: 56959.680 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Strain: ATCC MYA-4609 / Af293 / CBS 101355 / FGSC A1100 / Gene: sidA, Afu2g07680 / Production host: ![]() ![]() References: UniProt: E9QYP0, L-ornithine N5-monooxygenase [NAD(P)H] |
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-Non-polymers , 5 types, 1085 molecules ![](data/chem/img/ACT.gif)
![](data/chem/img/FAD.gif)
![](data/chem/img/NAP.gif)
![](data/chem/img/CA.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/FAD.gif)
![](data/chem/img/NAP.gif)
![](data/chem/img/CA.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-ACT / #3: Chemical | ChemComp-FAD / #4: Chemical | ChemComp-NAP / #5: Chemical | ChemComp-CA / #6: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.38 Å3/Da / Density % sol: 48.28 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion / pH: 7.5 Details: Enzyme stock solution: 8-10 mg/mL SidA and 1 mM NADP in 25 mM HEPES (pH 7.5) and 100 mM NaCl. Crystallization reservoir: 17-21 % PEG-3350, 0.1 M HEPES (pH 7.5), 0.1 M calcium acetate. Cryo- ...Details: Enzyme stock solution: 8-10 mg/mL SidA and 1 mM NADP in 25 mM HEPES (pH 7.5) and 100 mM NaCl. Crystallization reservoir: 17-21 % PEG-3350, 0.1 M HEPES (pH 7.5), 0.1 M calcium acetate. Cryo-buffer: 15 % PEG-200, 20 % PEG 3350, 0.1 M HEPES (pH 7.5), 0.1 M calcium acetate |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | ||||||||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | ||||||||||||||||||||||||||||||
Detector | Type: RDI CMOS_8M / Detector: CMOS / Date: Apr 27, 2016 | ||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1.00004 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||
Reflection | Resolution: 1.95→63.21 Å / Num. obs: 151085 / % possible obs: 99.5 % / Redundancy: 3.6 % / CC1/2: 0.997 / Rmerge(I) obs: 0.092 / Rpim(I) all: 0.056 / Rrim(I) all: 0.108 / Net I/σ(I): 12.1 / Num. measured all: 544409 / Scaling rejects: 2 | ||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 4B63 Resolution: 1.95→63.21 Å / SU ML: 0.21 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 20.21 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 83.9 Å2 / Biso mean: 30.1353 Å2 / Biso min: 6.28 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.95→63.21 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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