+Open data
-Basic information
Entry | Database: PDB / ID: 4uth | ||||||||||||
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Title | XenA - oxidized - Y183F variant | ||||||||||||
Components | NADH:flavin oxidoreductase | ||||||||||||
Keywords | OXIDOREDUCTASE | ||||||||||||
Function / homology | Function and homology information | ||||||||||||
Biological species | Pseudomonas putida (bacteria) | ||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.25 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. #1: Journal: J.Mol.Biol. / Year: 2010 Title: Determinants of Substrate Binding and Protonation in the Flavoenzyme Xenobiotic Reductase A. Authors: Spiegelhauer, O. / Werther, T. / Mende, S. / Knauer, S.H. / 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 | 4uth.cif.gz | 226.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4uth.ent.gz | 184.4 KB | Display | PDB format |
PDBx/mmJSON format | 4uth.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4uth_validation.pdf.gz | 807.4 KB | Display | wwPDB validaton report |
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Full document | 4uth_full_validation.pdf.gz | 807.4 KB | Display | |
Data in XML | 4uth_validation.xml.gz | 19 KB | Display | |
Data in CIF | 4uth_validation.cif.gz | 29.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ut/4uth ftp://data.pdbj.org/pub/pdb/validation_reports/ut/4uth | HTTPS FTP |
-Related structure data
Related structure data | 4utiC 4utjC 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
#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 / Variant: 86 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): K-12 / References: UniProt: A0A1X0ZT96, UniProt: Q3ZDM6*PLUS | ||||
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#2: Chemical | ChemComp-FMN / | ||||
#3: Chemical | #4: 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: 2.33 Å3/Da / Density % sol: 47.18 % / Description: NONE |
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: BESSY / Beamline: 14.2 / Wavelength: 0.91841 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.91841 Å / Relative weight: 1 |
Reflection | Resolution: 1.25→29.24 Å / Num. obs: 103079 / % possible obs: 99.6 % / Observed criterion σ(I): 1.96 / Redundancy: 3.6 % / Biso Wilson estimate: 9.45 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 14.01 |
-Processing
Software | Name: PHENIX / Version: (PHENIX.REFINE) / Classification: refinement | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.25→29.241 Å / SU ML: 0.1 / σ(F): 1.99 / Phase error: 16.14 / 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: 1.25→29.241 Å
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Refine LS restraints |
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LS refinement shell |
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