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- PDB-3db9: Crystal structure of UPF0317 protein Atu3911 from Agrobacterium t... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3db9 | ||||||
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Title | Crystal structure of UPF0317 protein Atu3911 from Agrobacterium tumefaciens. NorthEast Strcutural Genomics target AtR186 | ||||||
![]() | UPF0317 protein Atu3911 | ||||||
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Function / homology | ![]() | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Seetharaman, J. / Abashidze, M. / Wang, D. / Janjua, H. / Owens, L. / Xiao, R. / Liu, J. / Baran, M.C. / Acton, T.B. / Rost, B. ...Seetharaman, J. / Abashidze, M. / Wang, D. / Janjua, H. / Owens, L. / Xiao, R. / Liu, J. / Baran, M.C. / Acton, T.B. / Rost, B. / Montelione, G.T. / Hunt, J.F. / Tong, L. / Northeast Structural Genomics Consortium (NESG) | ||||||
![]() | ![]() Title: Crystal structure of UPF0317 protein Atu3911 from Agrobacterium tumefaciens. NorthEast Strcutural Genomics target AtR186 (CASP Target) Authors: Seetharaman, J. / Abashidze, M. / Wang, D. / Janjua, H. / Owens, L. / Xiao, R. / Liu, J. / Baran, M.C. / Acton, T.B. / Rost, B. / Montelione, G.T. / Hunt, J.F. / Tong, L. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 59.8 KB | Display | ![]() |
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PDB format | ![]() | 43.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 2pifS S: Starting model for refinement |
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Similar structure data | |
Other databases |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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2 |
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Unit cell |
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Components
#1: Protein | Mass: 28967.020 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Strain: Agrobacterium tumefaciens (strain C58 / ATCC 33970 / Gene: Atu3911, AGR_L_1868 / Plasmid: PET21 / Production host: ![]() ![]() ![]() |
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#2: Water | ChemComp-HOH / ![]() |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.16 Å3/Da / Density % sol: 43.03 % |
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Crystal grow![]() | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7 Details: 200 mM NH4SO4, 20% PEG 4000, 50 mM MOPS pH 7. VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: May 2, 2008 / Details: Mirrors |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 2.8→50 Å / Num. obs: 11899 / % possible obs: 99.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 21.8 % / Biso Wilson estimate: 105.8 Å2 / Rmerge(I) obs: 0.07 / Rsym value: 0.062 / Net I/σ(I): 17.9 |
Reflection shell | Resolution: 2.8→2.9 Å / Redundancy: 21 % / Rmerge(I) obs: 0.333 / Mean I/σ(I) obs: 16 / Num. unique all: 1183 / Rsym value: 0.361 / % possible all: 99.6 |
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Processing
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Refinement | Method to determine structure![]() ![]() Starting model: 2PIF.pdb Resolution: 2.8→38.94 Å / Rfactor Rfree error: 0.008 / Data cutoff high absF: 226034.91 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 67.4671 Å2 / ksol: 0.368438 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 54.4 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.8→38.94 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.8→2.98 Å / Rfactor Rfree error: 0.031 / Total num. of bins used: 6
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Xplor file |
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