+Open data
-Basic information
Entry | Database: PDB / ID: 2pwv | ||||||
---|---|---|---|---|---|---|---|
Title | tRNA guanine transglycosylase E235Q mutant in complex with preQ0 | ||||||
Components | Queuine tRNA-ribosyltransferase | ||||||
Keywords | TRANSFERASE / TGT / E235Q mutant / preQ0 | ||||||
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 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / AB INITIO / Resolution: 1.7 Å | ||||||
Authors | Tidten, N. / Stengl, B. / Heine, A. / Reuter, K. / Klebe, G. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2007 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 |
| ||||||
Remark 999 | sequence THERE IS A THR -> LYS SEQUENCE CONFLICT AT RESIDUE 312 IN THE UNIPROT DATABASE. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 2pwv.cif.gz | 91.7 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb2pwv.ent.gz | 67 KB | Display | PDB format |
PDBx/mmJSON format | 2pwv.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/pw/2pwv ftp://data.pdbj.org/pub/pdb/validation_reports/pw/2pwv | HTTPS FTP |
---|
-Related structure data
Related structure data | 2okoC 2potC 2pwuC 2qiiC 2z1vC 2z1wC 2z1xC 1p0bS S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| |||||||||
---|---|---|---|---|---|---|---|---|---|---|
1 |
| |||||||||
Unit cell |
| |||||||||
Components on special symmetry positions |
| |||||||||
Details | The second part of the biological assembly is generated by the two fold axis |
-Components
#1: Protein | Mass: 42924.719 Da / Num. of mol.: 1 / Mutation: E235Q Source method: isolated from a genetically manipulated source Source: (gene. exp.) Zymomonas mobilis (bacteria) / Gene: tgt / Plasmid: pET9d / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) pLysS References: UniProt: P28720, tRNA-guanosine34 preQ1 transglycosylase | ||
---|---|---|---|
#2: Chemical | ChemComp-ZN / | ||
#3: Chemical | ChemComp-PQ0 / | ||
#4: Chemical | ChemComp-GOL / #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.41 Å3/Da / Density % sol: 49.01 % |
---|---|
Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 5.5 Details: pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K |
-Data collection
Diffraction | Mean temperature: 113 K |
---|---|
Diffraction source | Source: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.54178 Å |
Detector | Type: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Aug 1, 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: 1.7→20 Å / Num. obs: 40368 / % possible obs: 0.983 % / Redundancy: 2.8 % / Rmerge(I) obs: 0.059 / Rsym value: 0.059 / Net I/σ(I): 12 |
Reflection shell | Resolution: 1.7→1.73 Å / Rmerge(I) obs: 0.491 / Mean I/σ(I) obs: 2.2 / Rsym value: 0.491 / % possible all: 0.969 |
-Processing
Software |
| |||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: AB INITIO Starting model: pdb entry 1P0B Resolution: 1.7→10 Å / Num. parameters: 12665 / Num. restraintsaints: 12244 / Cross valid method: FREE R / σ(F): 0 / Stereochemistry target values: Engh & Huber Details: ANISOTROPIC SCALING APPLIED BY THE METHOD OF PARKIN, MOEZZI & HOPE, J.APPL.CRYST.28(1995)53-56
| |||||||||||||||||||||||||||||||||
Solvent computation | Solvent model: BABINET (SWAT) | |||||||||||||||||||||||||||||||||
Refine analyze | Num. disordered residues: 2 / Occupancy sum hydrogen: 2812 / Occupancy sum non hydrogen: 3151 | |||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.7→10 Å
| |||||||||||||||||||||||||||||||||
Refine LS restraints |
|