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- PDB-3n55: SO1698 protein, an aspartic peptidase from Shewanella oneidensis. -
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Open data
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Basic information
Entry | Database: PDB / ID: 3n55 | |||||||||
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Title | SO1698 protein, an aspartic peptidase from Shewanella oneidensis. | |||||||||
![]() | (Peptidase) x 2 | |||||||||
![]() | HYDROLASE / structural genomics / aspartic peptidase / autocatalysis / PSI-2 / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG | |||||||||
Function / homology | ![]() | |||||||||
Biological species | ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Osipiuk, J. / Mulligan, R. / Collart, F. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG) | |||||||||
![]() | ![]() Title: Characterization of member of DUF1888 protein family, self-cleaving and self-assembling endopeptidase. Authors: Osipiuk, J. / Mulligan, R. / Bargassa, M. / Hamilton, J.E. / Cunningham, M.A. / Joachimiak, A. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 70.1 KB | Display | ![]() |
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PDB format | ![]() | 55.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 461.6 KB | Display | ![]() |
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Full document | ![]() | 462.8 KB | Display | |
Data in XML | ![]() | 9 KB | Display | |
Data in CIF | ![]() | 12.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3njfC ![]() 3njgC ![]() 3njhC ![]() 3njiC ![]() 3njjC ![]() 3njkC ![]() 3njlC ![]() 3njmC ![]() 3njnC C: citing same article ( |
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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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2 | ![]()
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Unit cell |
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Components
-Protein / Protein/peptide , 2 types, 2 molecules AB
#1: Protein | Mass: 12758.132 Da / Num. of mol.: 1 / Fragment: N-terminal domain 1-116 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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#2: Protein/peptide | Mass: 1080.217 Da / Num. of mol.: 1 / Fragment: C-terminal domain 117-125 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
-Non-polymers , 4 types, 143 molecules ![](data/chem/img/BME.gif)
![](data/chem/img/ACT.gif)
![](data/chem/img/ZN.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/ACT.gif)
![](data/chem/img/ZN.gif)
![](data/chem/img/HOH.gif)
#3: Chemical | ChemComp-BME / |
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#4: Chemical | ChemComp-ACT / |
#5: Chemical | ChemComp-ZN / |
#6: Water | ChemComp-HOH / |
-Details
Sequence details | THE CHAIN-B PEPTIDE IS A PRODUCT OF AUTOCATALY |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.51 Å3/Da / Density % sol: 64.93 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6 Details: 15% ETHANOL, 0.1 M MES BUFFER, 0.2 M ZINC ACETATE, pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 291K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 7, 2005 |
Radiation | Monochromator: double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9792 Å / Relative weight: 1 |
Reflection | Resolution: 1.57→32.9 Å / Num. obs: 27101 / % possible obs: 98.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 12.7 % / Biso Wilson estimate: 30.8 Å2 / Rmerge(I) obs: 0.051 / Χ2: 1.03 / Net I/σ(I): 17.8 |
Reflection shell | Resolution: 1.57→1.6 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.61 / Mean I/σ(I) obs: 1.66 / Num. unique all: 2466 / Χ2: 0.765 / % possible all: 84.1 |
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Processing
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Refinement | Method to determine structure: ![]() Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : RESIDUAL ONLY
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 59.52 Å2 / Biso mean: 20.372 Å2 / Biso min: 7.22 Å2
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Refinement step | Cycle: LAST / Resolution: 1.57→32.9 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.569→1.61 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Origin x: 1.0047 Å / Origin y: 21.124 Å / Origin z: 45.8209 Å
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