+Open data
-Basic information
Entry | Database: PDB / ID: 4ghr | ||||||
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Title | TGT D102N mutant in complex with lin-benzohypoxanthine inhibitor | ||||||
Components | Queuine tRNA-ribosyltransferase | ||||||
Keywords | TRANSFERASE/TRANSFERASE inhibitor / TIM BARREL / GLYCOSYLTRANSFERASE / QUEUOSINE / TRNA PROCESSING / BIOSYNTHESIS / 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 / AB INITIO / Resolution: 2 Å | ||||||
Authors | Immekus, F. / Klebe, G. | ||||||
Citation | Journal: To be Published Title: Protonation state analysis of the TGT active site Authors: Immekus, F. / Barandun, L.J. / 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 | 4ghr.cif.gz | 87.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4ghr.ent.gz | 62.7 KB | Display | PDB format |
PDBx/mmJSON format | 4ghr.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gh/4ghr ftp://data.pdbj.org/pub/pdb/validation_reports/gh/4ghr | HTTPS FTP |
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-Related structure data
Related structure data | 1p0dS 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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Details | HOMODIMER |
-Components
#1: Protein | Mass: 42924.719 Da / Num. of mol.: 1 / Mutation: T312K, D102N 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-ITE / |
#4: Chemical | ChemComp-GOL / |
#5: 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: 2.32 Å3/Da / Density % sol: 48.36 % |
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Crystal grow | Temperature: 288 K / Method: vapor diffusion, hanging drop / pH: 5.5 Details: 100MM 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: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å |
Detector | Type: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Feb 10, 2012 |
Radiation | Monochromator: Double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2→50 Å / Num. all: 26737 / Num. obs: 26737 / % possible obs: 97.7 % / Redundancy: 2.8 % / Biso Wilson estimate: 18.1 Å2 / Rsym value: 0.074 / Net I/σ(I): 14 |
Reflection shell | Resolution: 2→2.03 Å / Redundancy: 2.6 % / Mean I/σ(I) obs: 3.2 / Num. unique all: 1289 / Rsym value: 0.307 / % possible all: 96 |
-Processing
Software |
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Refinement | Method to determine structure: AB INITIO Starting model: 1P0D Resolution: 2→50 Å / Num. parameters: 11591 / Num. restraintsaints: 11130 / 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: 3 / Occupancy sum hydrogen: 2541 / Occupancy sum non hydrogen: 2874 | |||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2→50 Å
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Refine LS restraints |
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