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Yorodumi- PDB-7apm: tRNA-guanine transglycosylase H319C mutant spin-labeled with MTSL. -
+Open data
-Basic information
Entry | Database: PDB / ID: 7apm | ||||||
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Title | tRNA-guanine transglycosylase H319C mutant spin-labeled with MTSL. | ||||||
Components | Queuine tRNA-ribosyltransferase | ||||||
Keywords | TRANSFERASE / enzyme / spin label | ||||||
Function / homology | Function and homology information tRNA-guanosine34 preQ1 transglycosylase / tRNA-guanosine(34) queuine transglycosylase activity / tRNA-guanine transglycosylation / queuosine biosynthetic process / metal ion binding Similarity search - Function | ||||||
Biological species | Zymomonas mobilis subsp. mobilis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.66 Å | ||||||
Authors | Nguyen, D. / Heine, A. / Klebe, G. | ||||||
Funding support | Germany, 1items
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Citation | Journal: Angew.Chem.Int.Ed.Engl. / Year: 2021 Title: Unraveling a Ligand-Induced Twist of a Homodimeric Enzyme by Pulsed Electron-Electron Double Resonance. Authors: Nguyen, D. / Abdullin, D. / Heubach, C.A. / Pfaffeneder, T. / Nguyen, A. / Heine, A. / Reuter, K. / Diederich, F. / Schiemann, O. / Klebe, G. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7apm.cif.gz | 274.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7apm.ent.gz | 184.1 KB | Display | PDB format |
PDBx/mmJSON format | 7apm.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ap/7apm ftp://data.pdbj.org/pub/pdb/validation_reports/ap/7apm | HTTPS FTP |
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-Related structure data
Related structure data | 7aplC 1p0dS 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: 43186.980 Da / Num. of mol.: 1 / Mutation: C158S/C281S/H319R1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Zymomonas mobilis subsp. mobilis (strain ATCC 31821 / ZM4 / CP4) (bacteria) Strain: ATCC 31821 / ZM4 / CP4 / Gene: tgt, ZMO0363 / Plasmid: pPR-IBA2 / Production host: Escherichia coli BL21(DE3) (bacteria) References: UniProt: P28720, tRNA-guanosine34 preQ1 transglycosylase | ||||||
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#2: Chemical | ChemComp-ZN / | ||||||
#3: Chemical | #4: Chemical | ChemComp-CL / | #5: Water | ChemComp-HOH / | Has ligand of interest | Y | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.44 Å3/Da / Density % sol: 49.52 % |
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Crystal grow | Temperature: 291.15 K / Method: vapor diffusion, hanging drop / pH: 5.5 Details: 0.1 M MES, pH 5.5, 0.5 mM DTT, 13% PEG 8000, 10% DMSO |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.91841 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jan 31, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.91841 Å / Relative weight: 1 |
Reflection | Resolution: 1.66→45.68 Å / Num. obs: 47688 / % possible obs: 97.6 % / Redundancy: 3.4 % / Biso Wilson estimate: 18.45 Å2 / CC1/2: 0.997 / Rsym value: 0.075 / Net I/σ(I): 10.4 |
Reflection shell | Resolution: 1.66→1.76 Å / Redundancy: 3.2 % / Mean I/σ(I) obs: 2.1 / Num. unique obs: 7302 / CC1/2: 0.82 / Rsym value: 0.466 / % possible all: 92.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1P0D Resolution: 1.66→45.68 Å / SU ML: 0.1905 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 17.0193 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: 22.07 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.66→45.68 Å
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Refine LS restraints |
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LS refinement shell |
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