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Yorodumi- PDB-2ytz: Complex structure of Trm1 from Pyrococcus horikoshii with S-adeno... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2ytz | ||||||
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Title | Complex structure of Trm1 from Pyrococcus horikoshii with S-adenosyl-L-Homocystein in the orthorhombic crystal-lattice | ||||||
Components | N(2),N(2)-dimethylguanosine tRNA methyltransferase | ||||||
Keywords | TRANSFERASE / tRNA modification enzyme / guanine-26 / N(2)-N(2)-dimethyltransferase / Structural Genomics / NPPSFA / National Project on Protein Structural and Functional Analyses / RIKEN Structural Genomics/Proteomics Initiative / RSGI | ||||||
Function / homology | Function and homology information tRNA (guanine26-N2)-dimethyltransferase / tRNA (guanine(26)-N2)-dimethyltransferase activity / tRNA (guanine(10)-N2)-methyltransferase activity / tRNA methylation / tRNA binding Similarity search - Function | ||||||
Biological species | Pyrococcus horikoshii (archaea) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.65 Å | ||||||
Authors | Ihsanawati / Shirouzu, M. / Bessho, Y. / Yokoyama, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI) | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2008 Title: Crystal Structure of tRNA N(2),N(2)-Guanosine Dimethyltransferase Trm1 from Pyrococcus horikoshii Authors: Ihsanawati / Nishimoto, M. / Higashijima, K. / Shirouzu, M. / Grosjean, H. / 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 | 2ytz.cif.gz | 165.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2ytz.ent.gz | 129.6 KB | Display | PDB format |
PDBx/mmJSON format | 2ytz.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yt/2ytz ftp://data.pdbj.org/pub/pdb/validation_reports/yt/2ytz | HTTPS FTP |
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-Related structure data
Related structure data | 2dulSC 2ejtC 2ejuC S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data | |
Other databases |
-Links
-Assembly
Deposited unit |
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2 |
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3 |
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Unit cell |
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-Components
#1: Protein | Mass: 43010.938 Da / Num. of mol.: 2 / Fragment: residues 1-378 / Mutation: L1M Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pyrococcus horikoshii (archaea) / Gene: trm1 / Plasmid: pET11a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-CodonPlus (DE3)-RIL / References: UniProt: O59493, EC: 2.1.1.32 #2: Chemical | ChemComp-SO4 / #3: Chemical | #4: Water | ChemComp-HOH / | Sequence details | THE RESIDUE WAS ENGINEERED | |
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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: 3.05 Å3/Da / Density % sol: 59.72 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: 0.1M TrisCl, 2M Ammonium sulfate, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NW12A / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Nov 14, 2006 |
Radiation | Monochromator: Si / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.65→50 Å / Num. obs: 30188 / % possible obs: 96 % / Observed criterion σ(I): -3 / Redundancy: 7.11 % / Biso Wilson estimate: 31 Å2 / Rsym value: 0.095 / Net I/σ(I): 18.98 |
Reflection shell | Resolution: 2.65→2.74 Å / Mean I/σ(I) obs: 3.62 / Rsym value: 0.392 / % possible all: 87.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2DUL Resolution: 2.65→37.91 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 2085929.18 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 42.1559 Å2 / ksol: 0.37185 e/Å3 | ||||||||||||||||||||
Displacement parameters | Biso mean: 37 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.65→37.91 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.65→2.82 Å / Rfactor Rfree error: 0.019 / Total num. of bins used: 6
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Xplor file |
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