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Yorodumi- PDB-4pum: tRNA-Guanine Transglycosylase (TGT) Mutant D156N in Complex with ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4pum | ||||||
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Title | tRNA-Guanine Transglycosylase (TGT) Mutant D156N in Complex with 6-Amino-2-(methylamino)-1H,7H,8H-imidazo[4,5-g]quinazolin-8-one | ||||||
Components | Queuine tRNA-ribosyltransferase | ||||||
Keywords | transferase/transferase inhibitor / Transferase / Guanine Exchange Enzyme / preQ1 / tRNA / transferase-transferase inhibitor complex | ||||||
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: 1.93 Å | ||||||
Authors | Neeb, M. / Heine, A. / Klebe, G. | ||||||
Citation | Journal: J.Med.Chem. / Year: 2014 Title: Chasing Protons: How Isothermal Titration Calorimetry, Mutagenesis, and pKa Calculations Trace the Locus of Charge in Ligand Binding to a tRNA-Binding Enzyme. Authors: Neeb, M. / Czodrowski, P. / Heine, A. / Barandun, L.J. / Hohn, C. / 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 | 4pum.cif.gz | 162.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4pum.ent.gz | 125.4 KB | Display | PDB format |
PDBx/mmJSON format | 4pum.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/pu/4pum ftp://data.pdbj.org/pub/pdb/validation_reports/pu/4pum | HTTPS FTP |
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-Related structure data
Related structure data | 4pujC 4pukC 4pulC 4punC 1pudS 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: 43068.844 Da / Num. of mol.: 1 / Mutation: D156N 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: pPR-IBA2-ZM-D156N / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta2(DE3) References: UniProt: P28720, tRNA-guanosine34 preQ1 transglycosylase | ||||||
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#2: Chemical | ChemComp-ZN / | ||||||
#3: Chemical | #4: Chemical | ChemComp-2WU / | #5: Water | ChemComp-HOH / | Sequence details | AUTHORS HAVE INDICATED THAT THE CORRECT RESIDUE AT THE POSITION IS LYS (REUTER K.K.H., FICNER R.; J. ...AUTHORS HAVE INDICATED THAT THE CORRECT RESIDUE AT THE POSITION IS LYS (REUTER K.K.H., FICNER R.; J. BACTERIOL. 177:5284-5288(1995)) | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.38 Å3/Da / Density % sol: 48.3 % |
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Crystal grow | Temperature: 291.15 K / Method: vapor diffusion, sitting drop / pH: 5.5 Details: 100 mM MES, 10% DMSO, 13% PEG 8000, pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 291.15K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P14 (MX2) / Wavelength: 1.23953 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 20, 2012 |
Radiation | Monochromator: Double Crystal Monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.23953 Å / Relative weight: 1 |
Reflection | Resolution: 1.93→80 Å / Num. all: 30236 / Num. obs: 30236 / % possible obs: 99 % / Observed criterion σ(I): -3 / Redundancy: 4.7 % / Biso Wilson estimate: 25.8 Å2 / Rsym value: 0.047 / Net I/σ(I): 21.6 |
Reflection shell | Resolution: 1.93→1.98 Å / Redundancy: 4.6 % / Mean I/σ(I) obs: 3.4 / Rsym value: 0.505 / % possible all: 99.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1PUD Resolution: 1.93→70.668 Å / SU ML: 0.21 / σ(F): 1.99 / Phase error: 21.72 / 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: 1.93→70.668 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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