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Yorodumi- PDB-4fr6: tRNA-Guanine Transglycosylase cocrystallized with pyridyl-alkine-... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4fr6 | ||||||
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Title | tRNA-Guanine Transglycosylase cocrystallized with pyridyl-alkine-substituted lin-benzoguanine ligand | ||||||
Components | Queuine tRNA-ribosyltransferase | ||||||
Keywords | TRANSFERASE/TRANSFERASE inhibitor / TIM BARREL / GLYCOSYLTRANSFERASE / QUEUOSINE / BIOSYNTHESIS / TRANSFERASE / TRNA PROCESSING / TRNA / TRANSFERASE-TRANSFERASE inhibitor complex | ||||||
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: 1.59 Å | ||||||
Authors | Immekus, F. / Klebe, G. | ||||||
Citation | Journal: To be Published Title: Studies on TGT homodimer interface Authors: Immekus, F. / Barandun, L.J. / Betz, M. / Debaene, F. / Petiot, S. / Sanglier-Cianferani, S. / Diederich, F. / Klebe, G. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4fr6.cif.gz | 88.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4fr6.ent.gz | 63.4 KB | Display | PDB format |
PDBx/mmJSON format | 4fr6.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fr/4fr6 ftp://data.pdbj.org/pub/pdb/validation_reports/fr/4fr6 | HTTPS FTP |
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-Related structure data
Related structure data | 4fpsC 4fr1C 4fsaC 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
#1: Protein | Mass: 42925.703 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Zymomonas mobilis subsp. mobilis (bacteria) Strain: ATCC 31821 / ZM4 / CP4 / Gene: tgt, ZMO0363 / Plasmid: PET9D / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) References: UniProt: P28720, tRNA-guanosine34 preQ1 transglycosylase |
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#2: Chemical | ChemComp-ZN / |
#3: Chemical | ChemComp-0V3 / |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.29 Å3/Da / Density % sol: 46.03 % |
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Crystal grow | Temperature: 288 K / Method: vapor diffusion, hanging drop / pH: 5.5 Details: 100 MM MES, 1MM DTT, 10% DMSO, 13% PEG8000, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 288K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: BESSY / Beamline: 14.2 / Wavelength: 0.91841 Å |
Detector | Type: RAYONIX MX-225 / Detector: CCD / Date: Oct 19, 2010 / Details: Rh-coated silicon with indirect water cooling |
Radiation | Monochromator: Double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.91841 Å / Relative weight: 1 |
Reflection | Resolution: 1.59→30 Å / Num. all: 51448 / Num. obs: 51448 / % possible obs: 99.4 % / Redundancy: 3.3 % / Biso Wilson estimate: 14.54 Å2 / Rsym value: 0.035 / Net I/σ(I): 26.06 |
Reflection shell | Resolution: 1.59→1.62 Å / Redundancy: 3.3 % / Mean I/σ(I) obs: 11.92 / Num. unique all: 2576 / Rsym value: 0.091 / % possible all: 99.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: pdb entyr 1P0D Resolution: 1.59→30 Å / Num. parameters: 11663 / Num. restraintsaints: 11041 / Cross valid method: FREE R / σ(F): 0 / Stereochemistry target values: ENGH AND HUBER Details: ANISOTROPIC SCALING APPLIED BY THE METHOD OF PARKIN, MOEZZI & HOPE, J.APPL.CRYST.28(1995)53-56
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Refine analyze | Num. disordered residues: 11 / Occupancy sum hydrogen: 2485 / Occupancy sum non hydrogen: 2860 | |||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.59→30 Å
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Refine LS restraints |
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