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- PDB-1ixk: Crystal Structure Analysis of Methyltransferase Homolog Protein f... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1ixk | ||||||
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Title | Crystal Structure Analysis of Methyltransferase Homolog Protein from Pyrococcus Horikoshii | ||||||
![]() | Methyltransferase![]() | ||||||
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Function / homology | ![]() S-adenosylmethionine-dependent methyltransferase activity / rRNA processing / ![]() ![]() Similarity search - Function | ||||||
Biological species | ![]() ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Ishikawa, I. / Sakai, N. / Yao, M. / Watanabe, N. / Tamura, T. / Tanaka, I. | ||||||
![]() | ![]() Title: Crystal structure of human p120 homologue protein PH1374 from Pyrococcus horikoshii Authors: Ishikawa, I. / Sakai, N. / Tamura, T. / Yao, M. / Watanabe, N. / Tanaka, I. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 75.8 KB | Display | ![]() |
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PDB format | ![]() | 56.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | ![]() Mass: 36263.949 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() ![]() |
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#2: Water | ChemComp-HOH / ![]() |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.38 Å3/Da / Density % sol: 48.4 % | ||||||||||||||||||||||||||||||||||||
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Crystal grow![]() | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5 Details: PEG6000, Citric Acid, Glyserol, pH 5, VAPOR DIFFUSION, HANGING DROP, temperature 293K | ||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 20 ℃ / Method: vapor diffusion | ||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | ||||||||||||
Detector | Type: MARRESEARCH / Detector: CCD / Date: May 17, 2002 | ||||||||||||
Radiation | Monochromator: MIRROR + Si(111) / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||
Radiation wavelength |
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Reflection | Resolution: 1.9→24 Å / Num. all: 26780 / Num. obs: 26745 / % possible obs: 99 % / Redundancy: 5.7 % / Biso Wilson estimate: 39.1 Å2 / Rmerge(I) obs: 0.097 / Rsym value: 0.079 / Net I/σ(I): 6.8 | ||||||||||||
Reflection shell | Resolution: 1.9→2 Å / Redundancy: 5.7 % / Rmerge(I) obs: 0.331 / Mean I/σ(I) obs: 2.6 / Num. unique all: 3875 / Rsym value: 0.271 / % possible all: 98.6 | ||||||||||||
Reflection | *PLUS Lowest resolution: 23.77 Å / Num. measured all: 152004 | ||||||||||||
Reflection shell | *PLUS % possible obs: 98.6 % / Rmerge(I) obs: 0.329 |
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Processing
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Refinement | Method to determine structure![]() ![]()
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Solvent computation | Solvent model: throughout / Bsol: 49.4 Å2 / ksol: 0.511 e/Å3 | |||||||||||||||||||||||||||
Displacement parameters | Biso mean: 22.339 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.9→20 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 10 / % reflection obs: 99 %
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Xplor file | Serial no: 1 / Param file: protein_rep.param / Topol file: protein.top | |||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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