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- PDB-2r5r: The crystal structure of DUF198 from Nitrosomonas europaea ATCC 19718 -
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Open data
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Basic information
Entry | Database: PDB / ID: 2r5r | ||||||
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Title | The crystal structure of DUF198 from Nitrosomonas europaea ATCC 19718 | ||||||
![]() | UPF0343 protein NE1163 | ||||||
![]() | STRUCTURAL GENOMICS / UNKNOWN FUNCTION / APC86493 / DUF198 / Nitrosomonas europaea ATCC 19718 / PSI-2 / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG | ||||||
Function / homology | ![]() | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Tan, K. / Wu, R. / Nocek, B. / Bigelow, L. / Patterson, S. / Freeman, L. / Bargassa, M. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG) | ||||||
![]() | ![]() Title: The crystal structure of DUF198 from Nitrosomonas europaea ATCC 19718. Authors: Tan, K. / Wu, R. / Nocek, B. / Bigelow, L. / Patterson, S. / Freeman, L. / Bargassa, M. / 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 | ![]() | 57.7 KB | Display | ![]() |
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PDB format | ![]() | 45.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 448.5 KB | Display | ![]() |
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Full document | ![]() | 451.3 KB | Display | |
Data in XML | ![]() | 10.8 KB | Display | |
Data in CIF | ![]() | 13.4 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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1 | ![]()
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Unit cell |
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Details | Authors state that the biological unit is experimentally unknown. From molecular packing, it seems to be a tetramer, generated from symmetry operators given in remark 350. |
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Components
#1: Protein | Mass: 31201.350 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Species: Nitrosomonas europaea / Strain: IFO 14298 / Gene: NE1163 / Plasmid: pMCSG7 / Species (production host): Escherichia coli / Production host: ![]() ![]() |
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#2: Chemical | ChemComp-PO4 / |
#3: Chemical | ChemComp-IMD / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.69 Å3/Da / Density % sol: 66.66 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, sitting drop / pH: 4.2 Details: 1.6M NaH2PO4/0.4M K2HPO4, 0.1M Phosphate-Citrate, pH 4.2, VAPOR DIFFUSION, SITTING DROP, temperature 289K |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||
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Diffraction source | Source: ![]() ![]() ![]() | |||||||||
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 30, 2007 / Details: mirror | |||||||||
Radiation | Monochromator: Si 111 crystal / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||
Radiation wavelength |
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Reflection | Resolution: 3.05→38.87 Å / Num. all: 9363 / Num. obs: 9363 / % possible obs: 99.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 9.9 % / Rmerge(I) obs: 0.151 / Net I/σ(I): 17.4 | |||||||||
Reflection shell | Resolution: 3.05→3.16 Å / Redundancy: 7.9 % / Rmerge(I) obs: 0.847 / Mean I/σ(I) obs: 1.6 / Num. unique all: 846 / % possible all: 93.6 |
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Processing
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Refinement | Method to determine structure: ![]()
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 74.918 Å2
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Refinement step | Cycle: LAST / Resolution: 3.05→38.87 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 3.05→3.13 Å / Total num. of bins used: 20
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