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Yorodumi- PDB-2zig: Crystal Structure of TTHA0409, Putative DNA Modification Methylas... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2zig | ||||||
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Title | Crystal Structure of TTHA0409, Putative DNA Modification Methylase from Thermus thermophilus HB8 | ||||||
Components | Putative modification methylase | ||||||
Keywords | TRANSFERASE / MODIFICATION METHYLASE / METHYLTRANSFERASE / S-ADENOSYLMETHIONINE / THERMUS THERMOPHILUS / Structural Genomics / NPPSFA / National Project on Protein Structural and Functional Analyses / RIKEN Structural Genomics/Proteomics Initiative / RSGI | ||||||
Function / homology | Function and homology information site-specific DNA-methyltransferase (cytosine-N4-specific) activity / N-methyltransferase activity / DNA restriction-modification system / Transferases; Transferring one-carbon groups; Methyltransferases / methylation / DNA binding / cytoplasm Similarity search - Function | ||||||
Biological species | Thermus thermophilus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å | ||||||
Authors | Morita, R. / Ishikawa, H. / Nakagawa, N. / Masui, R. / Yokoyama, S. / Kuramitsu, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI) | ||||||
Citation | Journal: Proteins / Year: 2008 Title: Crystal structure of a putative DNA methylase TTHA0409 from Thermus thermophilus HB8 Authors: Morita, R. / Ishikawa, H. / Nakagawa, N. / Kuramitsu, S. / Masui, R. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2zig.cif.gz | 109.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2zig.ent.gz | 84.7 KB | Display | PDB format |
PDBx/mmJSON format | 2zig.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2zig_validation.pdf.gz | 434.9 KB | Display | wwPDB validaton report |
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Full document | 2zig_full_validation.pdf.gz | 448.9 KB | Display | |
Data in XML | 2zig_validation.xml.gz | 21.3 KB | Display | |
Data in CIF | 2zig_validation.cif.gz | 29.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zi/2zig ftp://data.pdbj.org/pub/pdb/validation_reports/zi/2zig | HTTPS FTP |
-Related structure data
Related structure data | 2zieSC 2zifC 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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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 34024.062 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thermus thermophilus (bacteria) / Strain: HB8 / Gene: TTHA0409 / Plasmid: pET-11a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q5SL84 #2: 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: 2.13 Å3/Da / Density % sol: 42.2 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.2 Details: 0.1M Tris HCl, 34% Ethanol, 25mM Mg Chloride, pH 8.2, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 95 K |
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL44B2 / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Feb 5, 2008 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→50 Å / Num. obs: 33368 / % possible obs: 99.6 % / Observed criterion σ(I): -3 / Redundancy: 3.7 % / Rmerge(I) obs: 0.044 / Rsym value: 0.028 / Net I/σ(I): 28.5 |
Reflection shell | Resolution: 2.1→2.18 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.377 / Mean I/σ(I) obs: 3.6 / Num. unique all: 3307 / Rsym value: 0.331 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2ZIE Resolution: 2.1→46.79 Å / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Bsol: 52.63 Å2 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 36.755 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.1→46.79 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.1→2.23 Å / Rfactor Rfree error: 0.017
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Xplor file |
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