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- PDB-1wzn: Crystal Structure of the SAM-dependent methyltransferase from Pyr... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1wzn | ||||||
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Title | Crystal Structure of the SAM-dependent methyltransferase from Pyrococcus horikoshii OT3 | ||||||
![]() | SAM-dependent methyltransferase | ||||||
![]() | TRANSFERASE / SAM-dependent methyltransferase / structural genomics / RIKEN Structural Genomics/Proteomics Initiative / RSGI | ||||||
Function / homology | ![]() S-adenosyl-L-methionine-dependent methyltransferases / Methyltransferase domain 25 / Methyltransferase domain / N-terminal domain of TfIIb / Single Sheet / Vaccinia Virus protein VP39 / S-adenosyl-L-methionine-dependent methyltransferase superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta Similarity search - Domain/homology | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Mizutani, H. / Kunishima, N. / RIKEN Structural Genomics/Proteomics Initiative (RSGI) | ||||||
![]() | ![]() Title: Crystal Structure of the SAM-dependent methyltransferase from Pyrococcus horikoshii OT3 Authors: Mizutani, H. / Kunishima, N. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 176.1 KB | Display | ![]() |
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PDB format | ![]() | 140 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.2 MB | Display | ![]() |
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Full document | ![]() | 1.2 MB | Display | |
Data in XML | ![]() | 36.1 KB | Display | |
Data in CIF | ![]() | 51.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Similar structure data | |
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Other databases |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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Unit cell |
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Components on special symmetry positions |
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Details | The biological assembly is a hexamer generated from the trimer in the asymmetric unit by the operations: x, 1-y, 1-z. |
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Components
#1: Protein | Mass: 29908.604 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() References: GenBank: 3257726, UniProt: O59000*PLUS, Transferases; Transferring one-carbon groups; Methyltransferases #2: Chemical | #3: Chemical | ChemComp-MG / | #4: Chemical | #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.9 Å3/Da / Density % sol: 57.8 % |
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Crystal grow | Temperature: 295 K / Method: microbatch / pH: 5.9 Details: PEG 3350, Magnesium sulfate, pH 5.9, microbatch, temperature 295K |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | ||||||||||||
Detector | Type: RIGAKU RAXIS V / Detector: IMAGE PLATE / Date: Jun 26, 2004 / Details: mirrors | ||||||||||||
Radiation | Monochromator: Bending magnet / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||
Radiation wavelength |
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Reflection | Resolution: 1.9→30 Å / Num. all: 81819 / Num. obs: 81819 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.12 % / Biso Wilson estimate: 17.3 Å2 / Rmerge(I) obs: 0.068 / Rsym value: 0.062 / Net I/σ(I): 12.2 | ||||||||||||
Reflection shell | Resolution: 1.9→1.97 Å / Redundancy: 6.07 % / Rmerge(I) obs: 0.352 / Mean I/σ(I) obs: 5.67 / Num. unique all: 8084 / Rsym value: 0.321 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]()
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 44.4224 Å2 / ksol: 0.36102 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 29.2 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.9→30 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.9→2.02 Å / Rfactor Rfree error: 0.011 / Total num. of bins used: 6
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Xplor file |
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