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Yorodumi- PDB-4utj: XenA - oxidized - Y183F variant in complex with 8-hydroxycoumarin -
+Open data
-Basic information
Entry | Database: PDB / ID: 4utj | |||||||||
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Title | XenA - oxidized - Y183F variant in complex with 8-hydroxycoumarin | |||||||||
Components | NADH:flavin oxidoreductase | |||||||||
Keywords | OXIDOREDUCTASE | |||||||||
Function / homology | Function and homology information | |||||||||
Biological species | Pseudomonas putida (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / OTHER / Resolution: 1.07 Å | |||||||||
Authors | Werther, T. / Dobbek, H. | |||||||||
Citation | Journal: Nat Commun / Year: 2017 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. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4utj.cif.gz | 233.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4utj.ent.gz | 192.6 KB | Display | PDB format |
PDBx/mmJSON format | 4utj.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4utj_validation.pdf.gz | 814.2 KB | Display | wwPDB validaton report |
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Full document | 4utj_full_validation.pdf.gz | 814.7 KB | Display | |
Data in XML | 4utj_validation.xml.gz | 20.5 KB | Display | |
Data in CIF | 4utj_validation.cif.gz | 31.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ut/4utj ftp://data.pdbj.org/pub/pdb/validation_reports/ut/4utj | HTTPS FTP |
-Related structure data
Related structure data | 4uthC 4utiC 4utkC 4utlC 4utmC 5lniC 5lnjC C: citing same article (ref.) |
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Similar structure data |
-Links
-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.) Pseudomonas putida (bacteria) / Gene: B7H19_27640 / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: A0A1X0ZT96, UniProt: Q3ZDM6*PLUS | ||||
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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: X-RAY DIFFRACTION |
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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: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.91841 |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.91841 Å / Relative weight: 1 |
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 |
-Processing
Software | Name: PHENIX / Version: (PHENIX.REFINE) / Classification: refinement | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Refinement | Method to determine structure: OTHER 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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