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- PDB-4tlx: Kutzneria sp. 744 ornithine N-hydroxylase, KtzI-FADred-NADP+-L-orn -
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Open data
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Basic information
Entry | Database: PDB / ID: 4tlx | ||||||
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Title | Kutzneria sp. 744 ornithine N-hydroxylase, KtzI-FADred-NADP+-L-orn | ||||||
![]() | KtzI | ||||||
![]() | OXIDOREDUCTASE / hydroxylase / flavin / ornithine / monooxygenase | ||||||
Function / homology | ![]() L-lysine N6-monooxygenase (NADPH) / L-lysine 6-monooxygenase (NADPH) activity / cellular biosynthetic process / : / intracellular iron ion homeostasis / nucleotide binding Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Setser, J.W. / Drennan, C.L. | ||||||
![]() | ![]() Title: Crystallographic Evidence of Drastic Conformational Changes in the Active Site of a Flavin-Dependent N-Hydroxylase. Authors: Setser, J.W. / Heemstra, J.R. / Walsh, C.T. / Drennan, C.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 | ![]() | 355.7 KB | Display | ![]() |
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PDB format | ![]() | 284.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 2.4 MB | Display | ![]() |
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Full document | ![]() | 2.5 MB | Display | |
Data in XML | ![]() | 67.9 KB | Display | |
Data in CIF | ![]() | 92.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4tlzC ![]() 4tm0C ![]() 4tm1C ![]() 4tm3C ![]() 4tm4C ![]() 3s5wS 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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Unit cell |
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Components
-Protein , 1 types, 4 molecules ABCD
#1: Protein | Mass: 49425.938 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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-Non-polymers , 5 types, 610 molecules ![](data/chem/img/FDA.gif)
![](data/chem/img/NAP.gif)
![](data/chem/img/ORN.gif)
![](data/chem/img/K.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/NAP.gif)
![](data/chem/img/ORN.gif)
![](data/chem/img/K.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-FDA / #3: Chemical | ChemComp-NAP / #4: Chemical | ChemComp-ORN / #5: Chemical | ChemComp-K / #6: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.73 Å3/Da / Density % sol: 54.98 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop Details: 0.9-1.15 M potassium thiocyanate, 22-25% PEG 3350, 0.1 M Bis-tris propane pH 8.5 Temp details: room temperature |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: PSI PILATUS 6M / Detector: PIXEL / Date: Apr 21, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 2.23→66 Å / Num. obs: 106307 / % possible obs: 99 % / Redundancy: 4.2 % / Rsym value: 0.065 / Net I/σ(I): 20.5 |
Reflection shell | Resolution: 2.23→2.27 Å / Redundancy: 4.3 % / Mean I/σ(I) obs: 2.7 / Rsym value: 0.572 / % possible all: 98.8 |
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Processing
Software | Name: PHENIX / Version: (phenix.refine: 1.9_1692) / Classification: refinement | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Refinement | Method to determine structure: ![]() Starting model: 3S5W Resolution: 2.23→49.819 Å / SU ML: 0.24 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.95 / 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 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.23→49.819 Å
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Refine LS restraints |
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LS refinement shell |
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