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Yorodumi- PDB-2zwv: Crystal structure of Thermus thermophilus 16S rRNA methyltransfer... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2zwv | ||||||
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Title | Crystal structure of Thermus thermophilus 16S rRNA methyltransferase RsmC (TTHA0533) | ||||||
Components | Probable ribosomal RNA small subunit methyltransferase | ||||||
Keywords | TRANSFERASE / METHYLTRANSFERASE / 16S RRNA METHYLTRANSFERASE / S-ADENOSYL-L-HOMOCYSTEINE / Structural Genomics / NPPSFA / National Project on Protein Structural and Functional Analyses / RIKEN Structural Genomics/Proteomics Initiative / RSGI | ||||||
Function / homology | Function and homology information rRNA (adenine-N6,N6-)-dimethyltransferase activity / tRNA processing / nucleic acid binding Similarity search - Function | ||||||
Biological species | Thermus thermophilus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å | ||||||
Authors | Wang, H. / Kawazoe, M. / Kaminishi, T. / Tatsuguchi, A. / Naoe, C. / Terada, T. / Shirouzu, M. / Takemoto, C. / Yokoyama, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI) | ||||||
Citation | Journal: to be published Title: Crystal structure of Thermus thermophilus 16S rRNA methyltransferase RsmC (TTHA0533) Authors: Wang, H. / Kawazoe, M. / Kaminishi, T. / Tatsuguchi, A. / Naoe, C. / Terada, T. / Shirouzu, M. / Takemoto, C. / Yokoyama, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2zwv.cif.gz | 90.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2zwv.ent.gz | 66.1 KB | Display | PDB format |
PDBx/mmJSON format | 2zwv.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zw/2zwv ftp://data.pdbj.org/pub/pdb/validation_reports/zw/2zwv | HTTPS FTP |
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-Related structure data
Related structure data | 2zulS S: Starting model for refinement |
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Similar structure data | |
Other databases |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 40708.914 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thermus thermophilus (bacteria) / Strain: HB8 / Gene: TTHA0533 / Plasmid: pET-11a / Production host: Escherichia coli (E. coli) / References: UniProt: Q5SKW0 |
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#2: Chemical | ChemComp-SAH / |
#3: 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: 2.31 Å3/Da / Density % sol: 46.81 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.9 Details: 0.4M Potassium sodium tartrate, 0.25% Polyethylene glycol MME 5000, 0.05M TRIS pH8.5, pH 8.9, 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: Mar 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→50 Å / Num. obs: 26313 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 7.2 % / Biso Wilson estimate: 3.9 Å2 / Rsym value: 0.14 / Net I/σ(I): 15 |
Reflection shell | Resolution: 2→2.07 Å / Redundancy: 7.2 % / Mean I/σ(I) obs: 3.7 / Num. unique all: 2555 / Rsym value: 0.506 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2ZUL Resolution: 2→38.72 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 58745.61 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 47.6129 Å2 / ksol: 0.378591 e/Å3 | ||||||||||||||||||||
Displacement parameters | Biso mean: 17.2 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2→38.72 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2→2.13 Å / Rfactor Rfree error: 0.012 / Total num. of bins used: 6
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Xplor file |
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