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Yorodumi- PDB-2oko: Z. mobilis tRNA guanine transglycosylase E235Q mutant apo-structu... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2oko | ||||||
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Title | Z. mobilis tRNA guanine transglycosylase E235Q mutant apo-structure at pH 5.5 | ||||||
Components | Queuine tRNA-ribosyltransferase | ||||||
Keywords | TRANSFERASE / tRNA guanine transglycosylase / TGT / PreQ0 / E235Q mutation | ||||||
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 / MOLECULAR REPLACEMENT / Resolution: 1.5 Å | ||||||
Authors | Tidten, N. | ||||||
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 |
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Remark 999 | SEQUENCE THE CONFLICT INVOLVING RESIDUE 311 IS CONSISTENT WITH THE REF. 1 AND 2 IN THE UNIPROT ...SEQUENCE THE CONFLICT INVOLVING RESIDUE 311 IS CONSISTENT WITH THE REF. 1 AND 2 IN THE UNIPROT SEQUENCE DATABASE, TGT_ZYMMO |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2oko.cif.gz | 178.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2oko.ent.gz | 139.9 KB | Display | PDB format |
PDBx/mmJSON format | 2oko.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ok/2oko ftp://data.pdbj.org/pub/pdb/validation_reports/ok/2oko | HTTPS FTP |
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-Related structure data
Related structure data | 2potC 2pwuC 2pwvC 2qiiC 2z1vC 2z1wC 2z1xC 1y5xS S: Starting model for refinement C: citing same article (ref.) |
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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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Details | The second part of the biological assembly is generated by the two fold axis |
-Components
#1: Protein | Mass: 42793.523 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 | ||
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#2: Chemical | ChemComp-ZN / | ||
#3: Chemical | ChemComp-GOL / #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.33 Å3/Da / Density % sol: 49.01 % |
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Crystal grow | pH: 5.5 / Details: pH 5.5 |
-Data collection
Diffraction source | Source: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 |
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Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Dec 13, 2006 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.5→50 Å / Num. obs: 210241 / % possible obs: 91.5 % / Redundancy: 3.5 % / Rmerge(I) obs: 0.1224 / Rsym value: 0.032 / Net I/σ(I): 33 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1Y5X Resolution: 1.5→10 Å / Num. parameters: 31053 / Num. restraintsaints: 38625 / 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 ANISOTROPIC REFINEMENT REDUCED FREE R (NO CUTOFF) BY ?
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Solvent computation | Solvent model: BABINET (SWAT) | |||||||||||||||||||||||||||||||||
Refine analyze | Num. disordered residues: 19 / Occupancy sum hydrogen: 2810 / Occupancy sum non hydrogen: 3355.5 | |||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.5→10 Å
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Refine LS restraints |
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