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- PDB-4utj: XenA - oxidized - Y183F variant in complex with 8-hydroxycoumarin -
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Open data
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Basic information
Entry | Database: PDB / ID: 4utj | |||||||||
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Title | XenA - oxidized - Y183F variant in complex with 8-hydroxycoumarin | |||||||||
![]() | NADH:flavin oxidoreductase | |||||||||
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Function / homology | ![]() | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | ![]() ![]() | |||||||||
![]() | Werther, T. / Dobbek, H. | |||||||||
![]() | ![]() Title: Redox-dependent substrate-cofactor interactions in the Michaelis-complex of a flavin-dependent oxidoreductase Authors: Werther, T. / Wahlefeld, S. / Salewski, J. / Kuhlmann, U. / Zebger, I. / Hildebrandt, P. / Dobbek, H. | |||||||||
History |
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Remark 700 | SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AB" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AB" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 8-STRANDED BARREL THIS IS REPRESENTED BY A 9-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 233.6 KB | Display | ![]() |
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PDB format | ![]() | 192.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 4uthC ![]() 4utiC ![]() 4utkC ![]() 4utlC ![]() 4utmC ![]() 5lniC ![]() 5lnjC 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
#1: Protein | Mass: 40093.223 Da / Num. of mol.: 1 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() | ||||
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#2: Chemical | ChemComp-FMN / ![]() | ||||
#3: Chemical | ChemComp-8CM / | ||||
#4: Chemical | ![]() #5: Water | ChemComp-HOH / | ![]() Sequence details | NO GENOMIC SEQUENCE DATA ARE AVAILABLE FOR THIS SPECIAL STRAIN. | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.36 Å3/Da / Density % sol: 47.8 % / Description: NONE |
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 1.07→29.28 Å / Num. obs: 165296 / % possible obs: 99.5 % / Observed criterion σ(I): 2 / Redundancy: 4 % / Biso Wilson estimate: 9.06 Å2 / Rmerge(I) obs: 0.05 |
Reflection shell | Resolution: 1.07→1.11 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.54 / Mean I/σ(I) obs: 2.54 / % possible all: 99.59 |
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Processing
Software | Name: PHENIX / Version: (PHENIX.REFINE) / Classification: refinement | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Refinement | Method to determine structure![]() Starting model: NONE Resolution: 1.07→29.28 Å / SU ML: 0.06 / σ(F): 1.99 / Phase error: 12.75 / 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: 1.07→29.28 Å
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Refine LS restraints |
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LS refinement shell |
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