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Open data
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Basic information
Entry | Database: PDB / ID: 7kpt | ||||||
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Title | Crystal structure of CtdE in complex with FAD and substrate 4 | ||||||
![]() | FAD-dependent monooxygenase CtdE | ||||||
![]() | BIOSYNTHETIC PROTEIN / FAD monooxygenase | ||||||
Function / homology | FLAVIN-ADENINE DINUCLEOTIDE / Chem-WU4![]() | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Zhao, B. / Hu, L. | ||||||
![]() | ![]() Title: Structural basis of the stereoselective formation of the spirooxindole ring in the biosynthesis of citrinadins. Authors: Liu, Z. / Zhao, F. / Zhao, B. / Yang, J. / Ferrara, J. / Sankaran, B. / Venkataram Prasad, B.V. / Kundu, B.B. / Phillips Jr., G.N. / Gao, Y. / Hu, L. / Zhu, T. / Gao, X. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 129.8 KB | Display | ![]() |
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PDB format | ![]() | 78.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1 MB | Display | ![]() |
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Full document | ![]() | 1 MB | Display | |
Data in XML | ![]() | 20.3 KB | Display | |
Data in CIF | ![]() | 30.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7kpqSC S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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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
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 49786.422 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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-Non-polymers , 5 types, 357 molecules ![](data/chem/img/FAD.gif)
![](data/chem/img/WU4.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/WU4.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-FAD / |
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#3: Chemical | ChemComp-WU4 / ( |
#4: Chemical | ChemComp-EDO / |
#5: Chemical | ChemComp-CL / |
#6: Water | ChemComp-HOH / |
-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.36 Å3/Da / Density % sol: 47.86 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop Details: 0.1M Calcium chloride, 20% w/v PEG 6000, 10% v/v Ethylene glycol |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 14, 2020 |
Radiation | Monochromator: Double-crystal Si(111) and multilayer / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9999 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→35 Å / Num. obs: 35699 / % possible obs: 98.7 % / Redundancy: 4.5 % / Biso Wilson estimate: 18.48 Å2 / Rmerge(I) obs: 0.078 / Rpim(I) all: 0.04 / Rrim(I) all: 0.088 / Net I/σ(I): 26.2 |
Reflection shell | Resolution: 1.9→1.93 Å / Redundancy: 4.6 % / Rmerge(I) obs: 0.849 / Mean I/σ(I) obs: 6 / Num. unique obs: 1774 / CC1/2: 0.811 / Rpim(I) all: 0.421 / Rrim(I) all: 0.949 / % possible all: 98.1 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 7KPQ Resolution: 1.91→34.02 Å / SU ML: 0.1709 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 19.3811 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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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 mean: 22.04 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.91→34.02 Å
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Refine LS restraints |
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LS refinement shell |
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