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- PDB-5mh0: Crystal structure of a DM9 domain containing protein from Crassos... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5mh0 | ||||||
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Title | Crystal structure of a DM9 domain containing protein from Crassostrea gigas | ||||||
![]() | Natterin-3 | ||||||
![]() | SUGAR BINDING PROTEIN / beta fold | ||||||
Function / homology | DM9 repeat / DM9 repeat / Repeats found in Drosophila proteins. / metal ion binding / Natterin-3![]() | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Weinert, T. / Warkentin, E. / Pang, G. | ||||||
![]() | ![]() Title: DM9 Domain Containing Protein Functions As a Pattern Recognition Receptor with Broad Microbial Recognition Spectrum. Authors: Jiang, S. / Wang, L. / Huang, M. / Jia, Z. / Weinert, T. / Warkentin, E. / Liu, C. / Song, X. / Zhang, H. / Witt, J. / Qiu, L. / Peng, G. / Song, 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 | ![]() | 96.2 KB | Display | ![]() |
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PDB format | ![]() | 74.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 427 KB | Display | ![]() |
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Full document | ![]() | 427 KB | Display | |
Data in XML | ![]() | 9.6 KB | Display | |
Data in CIF | ![]() | 13.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
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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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Components
#1: Protein | Mass: 15536.697 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() | ||
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#2: Chemical | #3: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.29 Å3/Da / Density % sol: 46.36 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 0.1M Tris-HCI, pH 7.0, 20% MME 2000 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: May 9, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.99999 Å / Relative weight: 1 |
Reflection | Resolution: 1.2→10 Å / Num. all: 45340 / Num. obs: 45250 / % possible obs: 99.8 % / Redundancy: 17.3 % / Rmerge(I) obs: 0.055 / Net I/σ(I): 25.7 |
Reflection shell | Resolution: 1.2→1.3 Å / Redundancy: 6.3 % / Rmerge(I) obs: 1.24 / Mean I/σ(I) obs: 3.1 / Num. measured obs: 9590 / Num. unique all: 9516 / % possible all: 99.2 |
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Processing
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Refinement | Method to determine structure: ![]()
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.24→9.968 Å
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Refine LS restraints |
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