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- PDB-2gsv: X-Ray Crystal Structure of Protein YvfG from Bacillus subtilis. N... -
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Open data
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Basic information
Entry | Database: PDB / ID: 2gsv | ||||||
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Title | X-Ray Crystal Structure of Protein YvfG from Bacillus subtilis. Northeast Structural Genomics Consortium Target SR478. | ||||||
![]() | Hypothetical protein yvfG | ||||||
![]() | STRUCTURAL GENOMICS / UNKNOWN FUNCTION / alpha-helical protein / PSI / Protein Structure Initiative / Northeast Structural Genomics Consortium / NESG | ||||||
Function / homology | Helix Hairpins - #40 / Uncharacterised domain YvfG / YvfG domain superfamily / YvfG protein / Helix Hairpins / Helix non-globular / Special / Uncharacterized protein YvfG![]() | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Forouhar, F. / Su, M. / Jayaraman, S. / Wang, D. / Fang, Y. / Cunningham, K. / Conover, K. / Ma, L.-C. / Xiao, R. / Acton, T.B. ...Forouhar, F. / Su, M. / Jayaraman, S. / Wang, D. / Fang, Y. / Cunningham, K. / Conover, K. / Ma, L.-C. / Xiao, R. / Acton, T.B. / Montelione, G.T. / Tong, L. / Hunt, J.F. / Northeast Structural Genomics Consortium (NESG) | ||||||
![]() | ![]() Title: Crystal Structure of the Hypothetical Protein YvfG from Bacillus subtilis, Northeast Structural Genomics Target SR478 Authors: Forouhar, F. / Su, M. / Jayaraman, S. / Wang, D. / Fang, Y. / Cunningham, K. / Conover, K. / Ma, L.-C. / 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 | ![]() | 38.2 KB | Display | ![]() |
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PDB format | ![]() | 29.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 452.7 KB | Display | ![]() |
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Full document | ![]() | 455.1 KB | Display | |
Data in XML | ![]() | 8.4 KB | Display | |
Data in CIF | ![]() | 10.7 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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2 | ![]()
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3 | ![]()
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Unit cell |
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Components on special symmetry positions |
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Components
#1: Protein | Mass: 9696.514 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #2: Chemical | #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.21 Å3/Da / Density % sol: 44.46 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 10mM Tris, 16% PEG3350, 180mM ammonium sulfate, 5mM DTT, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Apr 6, 2006 / Details: mirrors |
Radiation | Monochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→26.87 Å / Num. all: 26175 / Num. obs: 25914 / % possible obs: 99 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.9 % / Biso Wilson estimate: 12.1 Å2 / Rmerge(I) obs: 0.084 / Rsym value: 0.067 / Net I/σ(I): 14.98 |
Reflection shell | Resolution: 1.9→1.97 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.353 / Mean I/σ(I) obs: 3.4 / Num. unique all: 2645 / Rsym value: 0.284 / % possible all: 98.3 |
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Processing
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Refinement | Method to determine structure: ![]() Isotropic thermal model: OVERALL NCS RESTRAINTS. RMS SIGMA/WEIGHT Cross valid method: THROUGHOUT / σ(F): 2 / σ(I): 2 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 39.5435 Å2 / ksol: 0.349329 e/Å3 | |||||||||||||||||||||||||||
Displacement parameters | Biso mean: 36 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.9→26.87 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.9→2.02 Å / Rfactor Rfree error: 0.028 / Total num. of bins used: 6
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