+Open data
-Basic information
Entry | Database: PDB / ID: 1zjr | ||||||
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Title | Crystal Structure of A. aeolicus TrmH/SpoU tRNA modifying enzyme | ||||||
Components | tRNA (Guanosine-2'-O-)-methyltransferase | ||||||
Keywords | TRANSFERASE / methylase / RNA modifying enzyme / topological knot | ||||||
Function / homology | Function and homology information tRNA (guanosine18-2'-O)-methyltransferase / tRNA guanine ribose methylation / : / tRNA (uracil-2'-O-)-methyltransferase activity / tRNA binding Similarity search - Function | ||||||
Biological species | Aquifex aeolicus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 Å | ||||||
Authors | Pleshe, E. / Truesdell, J. / Batey, R.T. | ||||||
Citation | Journal: Acta Crystallogr.,Sect.F / Year: 2005 Title: Structure of a class II TrmH tRNA-modifying enzyme from Aquifex aeolicus. Authors: Pleshe, E. / Truesdell, J. / Batey, R.T. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1zjr.cif.gz | 57.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1zjr.ent.gz | 40.7 KB | Display | PDB format |
PDBx/mmJSON format | 1zjr.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zj/1zjr ftp://data.pdbj.org/pub/pdb/validation_reports/zj/1zjr | HTTPS FTP |
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-Related structure data
Related structure data | 1gz0S 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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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 24525.436 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Aquifex aeolicus (bacteria) / Gene: trmH, spoU / Plasmid: pTrxB / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta(DE3)/pLysS References: UniProt: O67577, tRNA (guanosine18-2'-O)-methyltransferase | ||
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#2: Chemical | ChemComp-SO4 / | ||
#3: Chemical | #4: 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: 2.79 Å3/Da / Density % sol: 55.5 % |
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Crystal grow | Temperature: 308 K / Method: vapor diffusion, hanging drop / pH: 4.4 Details: sodium citrate, ammonium sulfate, PEG 100, pH 4.4, VAPOR DIFFUSION, HANGING DROP, temperature 308K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 1.1271 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Jul 2, 2004 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.1271 Å / Relative weight: 1 |
Reflection | Resolution: 1.85→30 Å / Num. obs: 21822 / % possible obs: 95.3 % / Observed criterion σ(F): 2.9 / Observed criterion σ(I): 2.9 / Redundancy: 13.4 % / Biso Wilson estimate: 40.4 Å2 / Rmerge(I) obs: 0.058 / Net I/σ(I): 47.3 |
Reflection shell | Resolution: 1.85→1.92 Å / Rmerge(I) obs: 0.473 / Mean I/σ(I) obs: 2.9 / % possible all: 65 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: pdb entry 1GZ0 Resolution: 1.85→30 Å / σ(F): 2.9 / Stereochemistry target values: Engh & Huber
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Refine analyze | Luzzati coordinate error obs: 0.28 Å / Luzzati sigma a obs: 0.22 Å | |||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.85→30 Å
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Refine LS restraints |
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