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- PDB-3e23: Crystal structure of the RPA2492 protein in complex with SAM from... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3.0E+23 | ||||||
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Title | Crystal structure of the RPA2492 protein in complex with SAM from Rhodopseudomonas palustris, Northeast Structural Genomics Consortium Target RpR299 | ||||||
![]() | uncharacterized protein RPA2492 | ||||||
![]() | structural genomics / unknown function / alpha-beta protein / PSI-2 / Protein Structure Initiative / Northeast Structural Genomics Consortium / NESG | ||||||
Function / homology | Vaccinia Virus protein VP39 / S-adenosyl-L-methionine-dependent methyltransferase superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta / S-ADENOSYLMETHIONINE / Uncharacterized protein![]() | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Forouhar, F. / Chen, Y. / Seetharaman, J. / Mao, L. / Xiao, R. / Foote, E.L. / Ciccosanti, C. / Wang, H. / Tong, S. / Everett, J.K. ...Forouhar, F. / Chen, Y. / Seetharaman, J. / Mao, L. / Xiao, R. / Foote, E.L. / Ciccosanti, C. / Wang, H. / Tong, S. / Everett, J.K. / Acton, T.B. / Montelione, G.T. / Tong, L. / Hunt, J.F. / Northeast Structural Genomics Consortium (NESG) | ||||||
![]() | ![]() Title: Crystal structure of the RPA2492 protein in complex with SAM from Rhodopseudomonas palustris, Northeast Structural Genomics Consortium Target RpR299 Authors: Forouhar, F. / Chen, Y. / Seetharaman, J. / Mao, L. / Xiao, R. / Foote, E.L. / Ciccosanti, C. / Wang, H. / Tong, S. / K Everett, J. / Acton, T.B. / Montelione, G.T. / Tong, L. / Hunt, J.F. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 57.6 KB | Display | ![]() |
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PDB format | ![]() | 44.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 731.6 KB | Display | ![]() |
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Full document | ![]() | 732.9 KB | Display | |
Data in XML | ![]() | 13.5 KB | Display | |
Data in CIF | ![]() | 20.3 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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Unit cell |
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Components
#1: Protein | Mass: 23756.932 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Strain: CGA009 / Gene: RPA2492 / Plasmid: pET21 / Production host: ![]() ![]() | ||||
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#2: Chemical | ChemComp-SO4 / #3: Chemical | ChemComp-SAM / | #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.45 Å3/Da / Density % sol: 49.85 % |
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Crystal grow | Temperature: 277 K / pH: 7.5 Details: Protein solution: 10 mM Tris (pH 7.5), 100 mM sodium chloride, 5 mM DTT, and 5 mM S-adenosyl-methionine. Resevoir solution: 100 mM HEPES (pH 7.5) and 2 M ammonium sulfate. , microbatch under ...Details: Protein solution: 10 mM Tris (pH 7.5), 100 mM sodium chloride, 5 mM DTT, and 5 mM S-adenosyl-methionine. Resevoir solution: 100 mM HEPES (pH 7.5) and 2 M ammonium sulfate. , microbatch under oil, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Jul 28, 2008 / Details: mirrors |
Radiation | Monochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97902 Å / Relative weight: 1 |
Reflection | Resolution: 1.6→30 Å / Num. all: 60048 / Num. obs: 54164 / % possible obs: 90.2 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 4.1 % / Biso Wilson estimate: 9.9 Å2 / Rmerge(I) obs: 0.049 / Rsym value: 0.057 / Net I/σ(I): 33.94 |
Reflection shell | Resolution: 1.6→1.66 Å / Redundancy: 2.4 % / Rmerge(I) obs: 0.074 / Mean I/σ(I) obs: 12.77 / Num. unique all: 6000 / Rsym value: 0.109 / % possible all: 66.3 |
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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: 45.9086 Å2 / ksol: 0.4 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 13 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.6→19.86 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.6→1.66 Å / Rfactor Rfree error: 0.01 / Total num. of bins used: 10
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