+Open data
-Basic information
Entry | Database: PDB / ID: 2zzn | ||||||
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Title | The complex structure of aTrm5 and tRNACys | ||||||
Components |
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Keywords | TRANSFERASE/RNA / protein-RNA complex / TRANSFERASE-RNA COMPLEX | ||||||
Function / homology | Function and homology information tRNA methyltransferase activity / tRNA N1-guanine methylation / tRNA (guanine37-N1)-methyltransferase / tRNA (guanine(37)-N1)-methyltransferase activity / tRNA methylation / cytoplasm Similarity search - Function | ||||||
Biological species | Methanocaldococcus jannaschii (archaea) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.95 Å | ||||||
Authors | Goto-Ito, S. / Ito, T. / Yokoyama, S. | ||||||
Citation | Journal: Nat.Struct.Mol.Biol. / Year: 2009 Title: Tertiary structure checkpoint at anticodon loop modification in tRNA functional maturation. Authors: Goto-Ito, S. / Ito, T. / Kuratani, M. / Bessho, Y. / Yokoyama, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2zzn.cif.gz | 227 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2zzn.ent.gz | 175.4 KB | Display | PDB format |
PDBx/mmJSON format | 2zzn.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2zzn_validation.pdf.gz | 898.4 KB | Display | wwPDB validaton report |
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Full document | 2zzn_full_validation.pdf.gz | 954.1 KB | Display | |
Data in XML | 2zzn_validation.xml.gz | 35.8 KB | Display | |
Data in CIF | 2zzn_validation.cif.gz | 49.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zz/2zzn ftp://data.pdbj.org/pub/pdb/validation_reports/zz/2zzn | HTTPS FTP |
-Related structure data
Related structure data | 2zzmSC 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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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 39071.949 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Methanocaldococcus jannaschii (archaea) Plasmid: pET26b / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta2(DE3) / References: UniProt: Q58293 #2: RNA chain | Mass: 24129.359 Da / Num. of mol.: 2 / Source method: obtained synthetically Details: synthesized in vitro with the recombinant RNA polymerase of T7 phage References: GenBank: 6626255 #3: Chemical | #4: Chemical | ChemComp-MG / #5: Water | ChemComp-HOH / | |
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-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: 46.95 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 293 K / Method: sitting drop, vapor diffusion / pH: 7.5 Details: 87.5mM Mg(HCOO)2, 4.38% PEG 3350, 43.8mM CH3COONa pH 4.6, 8.8% MPD, 0.4mM CYMAL-5, 12.5mM Na-HEPES pH 7.5, sitting drop, vapor diffusion, temperature 293K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions |
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 3, 2007 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.95→50 Å / Num. obs: 25625 / Biso Wilson estimate: -0.1 Å2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2ZZM Resolution: 2.95→46.69 Å / Rfactor Rfree error: 0.008 / Occupancy max: 1 / Occupancy min: 1 / Data cutoff high absF: 14748571.75 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Details: BULK SOLVENT MODEL USED
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 37.1183 Å2 / ksol: 0.3 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 72.6 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.95→46.69 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.95→3.13 Å / Rfactor Rfree error: 0.025 / Total num. of bins used: 6
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Xplor file |
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