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Yorodumi- PDB-7f11: Crystal structure of NsrQ M128I in complex with substrate analogue 7 -
+Open data
-Basic information
Entry | Database: PDB / ID: 7f11 | ||||||
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Title | Crystal structure of NsrQ M128I in complex with substrate analogue 7 | ||||||
Components | NsrQ | ||||||
Keywords | ISOMERASE / tetrahydroxanthones / blennolides | ||||||
Function / homology | : / Oxidoreductases / NTF2-like domain superfamily / monooxygenase activity / Chem-0ER / Monooxygenase nsrQ Function and homology information | ||||||
Biological species | Aspergillus novofumigatus (mold) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å | ||||||
Authors | Yang, J. / Mori, T. / Abe, I. | ||||||
Citation | Journal: Angew.Chem.Int.Ed.Engl. / Year: 2021 Title: Structural Basis for Isomerization Reactions in Fungal Tetrahydroxanthone Biosynthesis and Diversification. Authors: Yang, J. / Mori, T. / Wei, X. / Matsuda, Y. / Abe, I. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7f11.cif.gz | 77.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7f11.ent.gz | 53.8 KB | Display | PDB format |
PDBx/mmJSON format | 7f11.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/f1/7f11 ftp://data.pdbj.org/pub/pdb/validation_reports/f1/7f11 | HTTPS FTP |
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-Related structure data
Related structure data | 7f0oSC 7f0yC 7f0zC 7f10C 7f13C 7f14C S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 19211.818 Da / Num. of mol.: 2 / Mutation: M128I Source method: isolated from a genetically manipulated source Source: (gene. exp.) Aspergillus novofumigatus (mold) / Production host: Escherichia coli (E. coli) / References: UniProt: A0A2I1C3W8 #2: Chemical | ChemComp-0ER / | #3: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.14 Å3/Da / Density % sol: 42.56 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / Details: 100 mM HEPES (pH7.5), 20% w/v PEG4000 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: BL-1A / Wavelength: 1.1 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Dec 19, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.1 Å / Relative weight: 1 |
Reflection | Resolution: 1.6→48.66 Å / Num. obs: 44119 / % possible obs: 99.9 % / Redundancy: 6.8 % / Biso Wilson estimate: 20.29 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.048 / Net I/σ(I): 19.6 |
Reflection shell | Resolution: 1.6→1.63 Å / Redundancy: 6.7 % / Rmerge(I) obs: 0.71 / Mean I/σ(I) obs: 2.2 / Num. unique obs: 2170 / CC1/2: 0.799 / % possible all: 97.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 7F0O Resolution: 1.6→48.66 Å / SU ML: 0.1886 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 22.7495 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: 26.74 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.6→48.66 Å
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Refine LS restraints |
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LS refinement shell |
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