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- PDB-2qti: Crystal structure of the UPF0352 protein SO_2176 from Shewanella ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 2qti | ||||||
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Title | Crystal structure of the UPF0352 protein SO_2176 from Shewanella oneidensis. NESG target SoR77. | ||||||
![]() | UPF0352 protein SO_2176 | ||||||
![]() | STRUCTURAL GENOMICS / UNKNOWN FUNCTION / Y2176_SHEON / UPF0352 / SO_2176 / PF07208 / NESG / SoR77 / PSI-2 / Protein Structure Initiative / Northeast Structural Genomics Consortium | ||||||
Function / homology | Uncharacterised protein family UPF0352 / YejL-like superfamily / Protein of unknown function (DUF1414) / YejL-like / YejL-like / Orthogonal Bundle / Mainly Alpha / UPF0352 protein SO_2176![]() | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Vorobiev, S.M. / Su, M. / Seetharaman, J. / Kuzin, A.P. / Wang, D. / Cunningham, K. / Owens, L. / Maglaqui, M. / Fang, Y. / Xiao, R. ...Vorobiev, S.M. / Su, M. / Seetharaman, J. / Kuzin, A.P. / Wang, D. / Cunningham, K. / Owens, L. / Maglaqui, M. / Fang, Y. / Xiao, R. / Acton, T.B. / Montelione, G.T. / Tong, L. / Hunt, J.F. / Northeast Structural Genomics Consortium (NESG) | ||||||
![]() | ![]() Title: Crystal structure of the UPF0352 protein SO_2176 from Shewanella oneidensis. Authors: Vorobiev, S.M. / Su, M. / Seetharaman, J. / Kuzin, A.P. / Wang, D. / Cunningham, K. / Owens, L. / Maglaqui, M. / Fang, Y. / Xiao, R. / 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 | ![]() | 21.2 KB | Display | ![]() |
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PDB format | ![]() | 15.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 420.5 KB | Display | ![]() |
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Full document | ![]() | 421.4 KB | Display | |
Data in XML | ![]() | 4.7 KB | Display | |
Data in CIF | ![]() | 5.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | |
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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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Unit cell |
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Details | Dimer by gel filtration. The second part of the biological assembly is generated by y, x, -z+1 symmetry operator. |
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Components
#1: Protein | Mass: 9040.045 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: 2.21 Å3/Da / Density % sol: 44.38 % Description: The structure factor file contains Friedel pairs |
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Crystal grow | Temperature: 291 K / Method: microbatch under oil / pH: 4 Details: 40% PEG 1000, 0.1M Ammonium phosphate, 0.1M Sodium citrate pH 4.0, MICROBATCH UNDER OIL, temperature 291.0K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Jul 25, 2007 |
Radiation | Monochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97913 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→50 Å / Num. all: 7182 / Num. obs: 7182 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 12.7 % / Biso Wilson estimate: 24.9 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 41.6 |
Reflection shell | Resolution: 2.3→2.38 Å / Redundancy: 8 % / Rmerge(I) obs: 0.527 / Mean I/σ(I) obs: 4.47 / Num. unique all: 721 / % possible all: 99.4 |
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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: 60.1581 Å2 / ksol: 0.397721 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 44.3 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.3→39.32 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.3→2.44 Å / Rfactor Rfree error: 0.021 / Total num. of bins used: 6
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Xplor file |
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