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- PDB-2gxf: X-Ray Crystal Structure of Protein YybH from Bacillus subtilis. N... -
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Open data
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Basic information
Entry | Database: PDB / ID: 2gxf | ||||||
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Title | X-Ray Crystal Structure of Protein YybH from Bacillus subtilis. Northeast Structural Genomics Consortium Target SR506. | ||||||
![]() | Hypothetical protein yybH | ||||||
![]() | STRUCTURAL GENOMICS / UNKNOWN FUNCTION / alpha-beta protein. / PSI / Protein Structure Initiative / Northeast Structural Genomics Consortium / NESG | ||||||
Function / homology | SnoaL-like domain / SnoaL-like domain / Nuclear Transport Factor 2; Chain: A, - #50 / NTF2-like domain superfamily / Nuclear Transport Factor 2; Chain: A, / Roll / Alpha Beta / Uncharacterized protein YybH![]() | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Forouhar, F. / Abashidze, M. / Jayaraman, S. / Cunningham, K. / Fang, Y. / Ma, L.-C. / Xiao, R. / Acton, T.B. / Montelione, G.T. / Hunt, J.F. ...Forouhar, F. / Abashidze, M. / Jayaraman, S. / Cunningham, K. / Fang, Y. / Ma, L.-C. / Xiao, R. / Acton, T.B. / Montelione, G.T. / Hunt, J.F. / Tong, L. / Northeast Structural Genomics Consortium (NESG) | ||||||
![]() | ![]() Title: Crystal Structure of the Hypothetical Protein YybH from Bacillus subtilis, Northeast Structural Genomics Target SR506 Authors: Forouhar, F. / Abashidze, M. / Jayaraman, S. / Cunningham, K. / Fang, Y. / Ma, L.-C. / Xiao, R. / Acton, T.B. / Montelione, G.T. / Hunt, J.F. / Tong, L. / Northeast Structural Genomics Consortium (NESG) | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 103.3 KB | Display | ![]() |
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PDB format | ![]() | 86.6 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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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: 16408.705 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #2: Chemical | ChemComp-MES / #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.46 Å3/Da / Density % sol: 49.94 % Description: THE STRUCTURE FACTOR FILE CONTAINS FRIEDEL PAIRS. |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.15 Details: 100mM MES (pH 6.15), 22% PEG5kMME, 200mM ammonium sulfate, and 5mM DTT., VAPOR DIFFUSION, HANGING DROP, temperature 291K |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | ||||||||||||
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Feb 28, 2006 / Details: mirrors. | ||||||||||||
Radiation | Monochromator: Si 111 CHANNEL / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||
Radiation wavelength |
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Reflection | Resolution: 3.1→29.42 Å / Num. all: 22751 / Num. obs: 22660 / % possible obs: 99.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5 % / Biso Wilson estimate: 46.3 Å2 / Rmerge(I) obs: 0.112 / Rsym value: 0.081 / Net I/σ(I): 15.17 | ||||||||||||
Reflection shell | Resolution: 3.1→3.21 Å / Redundancy: 5 % / Rmerge(I) obs: 0.585 / Mean I/σ(I) obs: 2.4 / Num. unique all: 2252 / Rsym value: 0.584 / % 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: 10 Å2 / ksol: 0.266245 e/Å3 | |||||||||||||||||||||||||
Displacement parameters | Biso mean: 52.4 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 3.1→29.42 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 3.1→3.29 Å / Rfactor Rfree error: 0.022 / Total num. of bins used: 6
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