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- PDB-2im8: X-Ray Crystal Structure of Protein yppE from Bacillus subtilis. N... -
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Open data
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Basic information
Entry | Database: PDB / ID: 2im8 | ||||||
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Title | X-Ray Crystal Structure of Protein yppE from Bacillus subtilis. Northeast Structural Genomics Consortium Target SR213. | ||||||
![]() | Hypothetical protein yppE | ||||||
![]() | STRUCTURAL GENOMICS / UNKNOWN FUNCTION / SR213 / yppE / PSI-2 / Protein Structure Initiative / Northeast Structural Genomics Consortium / NESG | ||||||
Function / homology | YppE-like / YppE-like / YppE-like superfamily / Bacterial domain of unknown function (DUF1798) / Four Helix Bundle (Hemerythrin (Met), subunit A) / Up-down Bundle / Mainly Alpha / PHOSPHATE ION / Uncharacterized protein YppE![]() | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Kuzin, A.P. / Shastry, R. / Janjua, H. / Cunningham, K. / Ma, L.C. / Xiao, R. / Liu, J. / Hang, D. / Baran, M.C. / Acton, T.B. ...Kuzin, A.P. / Shastry, R. / Janjua, H. / Cunningham, K. / Ma, L.C. / Xiao, R. / Liu, J. / Hang, D. / Baran, M.C. / Acton, T.B. / Rost, B. / Montelione, G.T. / Tong, L. / Hunt, J.F. / Northeast Structural Genomics Consortium (NESG) | ||||||
![]() | ![]() Title: X-Ray structure of hypothetical protein yPPE. Northeast Structural Genomics Consortium target SR213. Authors: Kuzin, A.P. / Neely, H. / Seetharaman, J. / Shastry, R. / Janjua, H. / Cunningham, K. / Ma, L.C. / Xiao, R. / Liu, J. / Baran, M.C. / Acton, T.B. / Rost, B. / Montelione, G. / 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 | ![]() | 60.3 KB | Display | ![]() |
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PDB format | ![]() | 48.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 448.3 KB | Display | ![]() |
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Full document | ![]() | 452.5 KB | Display | |
Data in XML | ![]() | 13.1 KB | Display | |
Data in CIF | ![]() | 17.9 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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2 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 15695.204 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #2: Chemical | ChemComp-PO4 / | #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 1.92 Å3/Da / Density % sol: 36.06 % Description: THE STRUCTURE FACTOR FILE CONTAINS FRIEDEL PAIRS |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 0.8M KH2PO4, 0.8M NaH2PO4, 0.1M HEPES, pH 7.5, VAPOR DIFFUSION, SITTING 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: Aug 24, 2006 / Details: mirrors | ||||||||||||
Radiation | Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||
Radiation wavelength |
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Reflection | Resolution: 2→30 Å / Num. obs: 30962 / % possible obs: 97.7 % / Observed criterion σ(I): -3 / Redundancy: 33.6 % / Biso Wilson estimate: 19 Å2 / Rmerge(I) obs: 0.075 / Net I/σ(I): 29.2 | ||||||||||||
Reflection shell | Resolution: 2→2.07 Å / Rmerge(I) obs: 0.334 / Mean I/σ(I) obs: 7.5 / % possible all: 93.4 |
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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: 42.5853 Å2 / ksol: 0.357933 e/Å3 | ||||||||||||||||||||
Displacement parameters | Biso mean: 27.9 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2→19.29 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2→2.13 Å / Rfactor Rfree error: 0.031 / Total num. of bins used: 6
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Xplor file |
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