+Open data
-Basic information
Entry | Database: PDB / ID: 4utk | |||||||||
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Title | XenA - reduced - Y183F variant | |||||||||
Components | XENOBIOTIC REDUCTASE | |||||||||
Keywords | OXIDOREDUCTASE | |||||||||
Function / homology | Function and homology information | |||||||||
Biological species | PSEUDOMONAS PUTIDA (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.44 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 | 4utk.cif.gz | 226.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4utk.ent.gz | 184.3 KB | Display | PDB format |
PDBx/mmJSON format | 4utk.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4utk_validation.pdf.gz | 829.2 KB | Display | wwPDB validaton report |
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Full document | 4utk_full_validation.pdf.gz | 830.3 KB | Display | |
Data in XML | 4utk_validation.xml.gz | 19.2 KB | Display | |
Data in CIF | 4utk_validation.cif.gz | 29.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ut/4utk ftp://data.pdbj.org/pub/pdb/validation_reports/ut/4utk | HTTPS FTP |
-Related structure data
Related structure data | 4uthC 4utiC 4utjC 4utlC 4utmC 5lniC 5lnjC 3l5lS C: citing same article (ref.) S: Starting model for refinement |
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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) / Strain: 86 / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: Q3ZDM6, NADPH dehydrogenase | ||||
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#2: Chemical | ChemComp-FNR / | ||||
#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: 2.36 Å3/Da / Density % sol: 47.83 % / 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: 1.44→28.84 Å / Num. obs: 68214 / % possible obs: 99 % / Observed criterion σ(I): 2.25 / Redundancy: 3.6 % / Biso Wilson estimate: 12.71 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 13.63 |
Reflection shell | Resolution: 1.44→1.49 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.58 / Mean I/σ(I) obs: 2.25 / % possible all: 99.54 |
-Processing
Software | Name: PHENIX / Version: (PHENIX.REFINE) / Classification: refinement | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3L5L Resolution: 1.44→28.835 Å / SU ML: 0.12 / σ(F): 1.99 / Phase error: 16.25 / 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: 1.44→28.835 Å
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Refine LS restraints |
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LS refinement shell |
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