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Yorodumi- PDB-2zie: Crystal Structure of TTHA0409, Putatative DNA Modification Methyl... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2zie | ||||||
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Title | Crystal Structure of TTHA0409, Putatative DNA Modification Methylase from Thermus thermophilus HB8- Selenomethionine derivative | ||||||
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 / MAD / Resolution: 2.5 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 | 2zie.cif.gz | 101.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2zie.ent.gz | 83.7 KB | Display | PDB format |
PDBx/mmJSON format | 2zie.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2zie_validation.pdf.gz | 437.5 KB | Display | wwPDB validaton report |
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Full document | 2zie_full_validation.pdf.gz | 452.9 KB | Display | |
Data in XML | 2zie_validation.xml.gz | 20.3 KB | Display | |
Data in CIF | 2zie_validation.cif.gz | 27.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zi/2zie ftp://data.pdbj.org/pub/pdb/validation_reports/zi/2zie | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 34164.746 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): B834(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: 2.11 Å3/Da / Density % sol: 41.78 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.6 Details: 0.1M Tris HCl, 38% Ethanol, 25mM Mg Chloride, pH 8.6, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 95 K | ||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B2 / Wavelength: 0.97887, 0.90000, 0.97946 | ||||||||||||
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Oct 6, 2007 | ||||||||||||
Radiation | Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||
Radiation wavelength |
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Reflection | Resolution: 2.5→50 Å / Num. obs: 19995 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 5.2 % / Rmerge(I) obs: 0.071 / Rsym value: 0.057 / Net I/σ(I): 27.2 | ||||||||||||
Reflection shell | Resolution: 2.5→2.59 Å / Redundancy: 5.3 % / Rmerge(I) obs: 0.291 / Mean I/σ(I) obs: 5.1 / Num. unique all: 1979 / Rsym value: 0.271 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MAD / Resolution: 2.5→19.92 Å / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Displacement parameters | Biso mean: 37.4 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.5→19.92 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.5→2.66 Å / Rfactor Rfree error: 0.02
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