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- PDB-2dlb: X-ray Crystal Structure of Protein yopT from Bacillus subtilis. N... -
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Open data
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Basic information
Entry | Database: PDB / ID: 2dlb | ||||||
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Title | X-ray Crystal Structure of Protein yopT from Bacillus subtilis. Northeast Structural Genomics Consortium Target SR412 | ||||||
![]() | yopT | ||||||
![]() | STRUCTURAL GENOMICS / UNKNOWN FUNCTION / sr412 / NESG / PSI / Protein Structure Initiative / Northeast Structural Genomics Consortium | ||||||
Function / homology | Protein of unknown function YopT / Protein of unknown function YopT / YopT domain superfamily / Hypothetical protein Yopt / Ubiquitin-like (UB roll) / Roll / Alpha Beta / SPbeta prophage-derived uncharacterized protein YopT![]() | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Kuzin, A.P. / Chen, Y. / Seetharaman, J. / Ho, C.-K. / Cunningham, K. / Janjua, H. / Conover, K. / Ma, L.-C. / Xiao, R. / Acton, T.B. ...Kuzin, A.P. / Chen, Y. / Seetharaman, J. / Ho, C.-K. / Cunningham, K. / Janjua, H. / Conover, K. / Ma, L.-C. / Xiao, R. / Acton, T.B. / Montelione, G.T. / Hunt, J.F. / Tong, L. / Northeast Structural Genomics Consortium (NESG) | ||||||
![]() | ![]() Title: X-ray structure of hypothetical protein from Bacillus subtilis O34498 at the resolution of 1.2A. NESG target SR412 Authors: Kuzin, A.P. / Chen, Y. / Seetharaman, J. / Ho, C.-K. / Cunningham, K. / Janjua, H. / Conover, K. / Ma, L.-C. / Xiao, R. / Acton, T.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 | ![]() | 72.5 KB | Display | ![]() |
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PDB format | ![]() | 57.3 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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Unit cell |
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Details | In according to Dynamic Light Scattering SR412 is dimer. |
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Components
#1: Protein | Mass: 9249.060 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #2: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.71 Å3/Da / Density % sol: 52.83 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 4 Details: 0.1M lithium sulfate, 0.1M sodium citrate, 20% PEG 4000, VAPOR DIFFUSION, HANGING DROP, temperature 277K, pH 4.0 |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | ||||||||||||
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Mar 9, 2006 / Details: mirrors | ||||||||||||
Radiation | Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||
Radiation wavelength |
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Reflection | Resolution: 1.2→30 Å / Num. all: 53757 / Num. obs: 53730 / % possible obs: 87.5 % / Observed criterion σ(I): -3 | ||||||||||||
Reflection shell | Resolution: 1.2→1.24 Å / % possible all: 59.6 |
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Processing
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Refinement | Method to determine structure: AB INITIO / Resolution: 1.2→30 Å / Num. parameters: 11721 / Num. restraintsaints: 14189 / Cross valid method: FREE R / σ(F): 0 / Stereochemistry target values: ENGH AND HUBER Details: Anisotropic refinement reduced free r (no cutoff) by
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Refine analyze | Num. disordered residues: 6 / Occupancy sum hydrogen: 1100.5 / Occupancy sum non hydrogen: 1281 | |||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.2→30 Å
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Refine LS restraints |
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