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Open data
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Basic information
Entry | Database: PDB / ID: 2z1v | ||||||
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Title | tRNA guanine transglycosylase E235Q mutant apo structure, pH 8.5 | ||||||
![]() | Queuine tRNA-ribosyltransferase | ||||||
![]() | TRANSFERASE / tRNA guanine transglycosylase / TGT / E235Q mutant / apo / pH 8.5 | ||||||
Function / homology | ![]() 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 | ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Tidten, N. / Stengl, B. / Heine, A. / Garcia, G.A. / Klebe, G. / Reuter, K. | ||||||
![]() | ![]() Title: Glutamate versus Glutamine Exchange Swaps Substrate Selectivity in tRNA-Guanine Transglycosylase: Insight into the Regulation of Substrate Selectivity by Kinetic and Crystallographic Studies Authors: Tidten, N. / Stengl, B. / Heine, A. / Garcia, G.A. / Klebe, G. / Reuter, K. | ||||||
History |
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Remark 999 | SEQUENCE THE CONFLICT INVOLVING RESIDUE 312 IS CONSISTENT WITH THE REF. 1 AND 2 IN THE UNIPROT ...SEQUENCE THE CONFLICT INVOLVING RESIDUE 312 IS CONSISTENT WITH THE REF. 1 AND 2 IN THE UNIPROT SEQUENCE DATABASE, TGT_ZYMMO. |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 172.5 KB | Display | ![]() |
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PDB format | ![]() | 134.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 2okoSC ![]() 2potC ![]() 2pwuC ![]() 2pwvC ![]() 2qiiC ![]() 2z1wC ![]() 2z1xC S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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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: 42924.719 Da / Num. of mol.: 1 / Mutation: E235Q Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: P28720, tRNA-guanosine34 preQ1 transglycosylase | ||
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#2: Chemical | ChemComp-ZN / | ||
#3: Chemical | ChemComp-GOL / #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.41 Å3/Da / Density % sol: 49.01 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: 5% PEG 8000, 100mM Tris/HCl pH 8.5, 1mM DTT, 10% DMSO, pH 8.50, VAPOR DIFFUSION, HANGING DROP, temperature 291K |
-Data collection
Diffraction | Mean temperature: 113 K |
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Diffraction source | Source: ![]() |
Detector | Type: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Jul 12, 2006 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54178 Å / Relative weight: 1 |
Reflection | Resolution: 1.55→20 Å / Num. obs: 56093 / % possible obs: 95.6 % / Redundancy: 2.3 % / Rmerge(I) obs: 0.058 / Rsym value: 0.058 / Net I/σ(I): 16 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 2OKO Resolution: 1.55→20 Å / Num. parameters: 29142 / Num. restraintsaints: 36058 / Cross valid method: FREE R / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: BABINET (SWAT) | |||||||||||||||||||||||||||||||||
Refine analyze | Num. disordered residues: 7 / Occupancy sum hydrogen: 2823 / Occupancy sum non hydrogen: 3205.5 | |||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.55→20 Å
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Refine LS restraints |
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