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Yorodumi- PDB-6fmn: tRNA guanine Transglycosylase (TGT) in co-crystallized complex wi... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6fmn | ||||||
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Title | tRNA guanine Transglycosylase (TGT) in co-crystallized complex with 6-amino-2-((((2R,3S,4R,5R)-3,4-dihydroxy-5-methoxytetrahydrofuran-2-yl)methyl)amino)-1,7-dihydro-8H-imidazo[4,5-g]quinazolin-8-one | ||||||
Components | Queuine tRNA-ribosyltransferase | ||||||
Keywords | TRANSFERASE / CO-CRYSTALLIZATION / CARBOHYDRATES / TRANSFERASE INHIBITOR | ||||||
Function / homology | Function and homology information tRNA-guanosine34 preQ1 transglycosylase / tRNA wobble guanine modification / tRNA-guanosine(34) queuine transglycosylase activity / tRNA-guanine transglycosylation / queuosine biosynthetic process / metal ion binding / cytosol Similarity search - Function | ||||||
Biological species | Zymomonas mobilis subsp. mobilis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.36 Å | ||||||
Authors | Nguyen, A. / Heine, A. / Klebe, G. | ||||||
Citation | Journal: Chemistry / Year: 2018 Title: Sugar Acetonides are a Superior Motif for Addressing the Large, Solvent-Exposed Ribose-33 Pocket of tRNA-Guanine Transglycosylase. Authors: Movsisyan, L.D. / Schafer, E. / Nguyen, A. / Ehrmann, F.R. / Schwab, A. / Rossolini, T. / Zimmerli, D. / Wagner, B. / Daff, H. / Heine, A. / Klebe, G. / Diederich, F. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6fmn.cif.gz | 242 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6fmn.ent.gz | 197 KB | Display | PDB format |
PDBx/mmJSON format | 6fmn.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fm/6fmn ftp://data.pdbj.org/pub/pdb/validation_reports/fm/6fmn | HTTPS FTP |
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-Related structure data
Related structure data | 6fpuC 1pudS S: Starting model for refinement 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
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 42925.703 Da / Num. of mol.: 1 / Mutation: T312K 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 / Production host: Escherichia coli (E. coli) References: UniProt: P28720, tRNA-guanosine34 preQ1 transglycosylase |
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-Non-polymers , 5 types, 421 molecules
#2: Chemical | #3: Chemical | ChemComp-CL / | #4: Chemical | ChemComp-ZN / | #5: Chemical | ChemComp-E4E / | #6: Water | ChemComp-HOH / | |
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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: 2.4 Å3/Da / Density % sol: 48 % |
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Crystal grow | Temperature: 288 K / Method: vapor diffusion, hanging drop / pH: 5.5 / Details: 13% PEG 8000,100MM MES, 10%, DMSO, PH 5.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.9184 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jan 27, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9184 Å / Relative weight: 1 |
Reflection | Resolution: 1.34→44.77 Å / Num. obs: 86836 / % possible obs: 96.9 % / Redundancy: 3.3 % / Rrim(I) all: 0.097 / Rsym value: 0.081 / Net I/σ(I): 9 |
Reflection shell | Resolution: 1.34→1.42 Å / Mean I/σ(I) obs: 2 / Num. unique obs: 13420 / Rrim(I) all: 0.539 / Rsym value: 0.446 / % possible all: 93.1 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1PUD Resolution: 1.36→44.768 Å / SU ML: 0.12 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 13.18
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.36→44.768 Å
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Refine LS restraints |
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LS refinement shell |
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